diff --git a/NEWS.md b/NEWS.md
index b8fe0af7a5b7dc87cf1d8256215be4ec9a6b3a3d..3c8dc25f0f020aac62e3a898d33659a4038fc85c 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+# Version 1.6.0 (2018-11-01)
+
+Bioconductor 3.8 release
+
## Version 1.5.8 (2018-10-22)
* Add WithSpikes argument when calling BASiCS::BASiCS_MCMC()
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index e34f9ab855eac742864413ffaa3de39661bb1012..ee9faac7e27f403eaec07c2226569fc9ad9e21f2 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -70,7 +70,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 447597f8363f54c0332afb9fea60c801782d3ea4..be929e705b95fa70d1b03f631eb7c2f733220290 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -70,7 +70,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/articles/splatter.html b/docs/articles/splatter.html
index 927f135ea27128de37a78dbbdeedef0a0106c4db..260abc2e3a777c5a7d1bd51ee226910ae7e94958 100644
--- a/docs/articles/splatter.html
+++ b/docs/articles/splatter.html
@@ -36,7 +36,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
@@ -80,7 +80,7 @@
<h1>Introduction to Splatter</h1>
<h4 class="author">Luke Zappia</h4>
- <h4 class="date">2018-10-22</h4>
+ <h4 class="date">2018-11-02</h4>
<small class="dont-index">Source: <a href="https://github.com/Oshlack/splatter/blob/master/vignettes/splatter.Rmd"><code>vignettes/splatter.Rmd</code></a></small>
<div class="hidden name"><code>splatter.Rmd</code></div>
@@ -187,7 +187,7 @@
<pre><code>## Simulating library sizes...</code></pre>
<pre><code>## Simulating gene means...</code></pre>
<pre><code>## Simulating BCV...</code></pre>
-<pre><code>## Simulating counts...</code></pre>
+<pre><code>## Simulating counts..</code></pre>
<pre><code>## Simulating dropout (if needed)...</code></pre>
<pre><code>## Done!</code></pre>
<p>These steps will be explained in detail in the following sections but briefly the first step takes a dataset and estimates simulation parameters from it and the second step takes those parameters and simulates a new dataset.</p>
@@ -329,7 +329,7 @@
##
## Global:
## (Genes) (Cells) [Seed]
-## 10000 100 926367
+## 10000 100 477689
##
## 28 additional parameters
##
@@ -402,7 +402,7 @@
##
## Global:
## (GENES) (Cells) [Seed]
-## 8000 100 926367
+## 8000 100 477689
##
## 28 additional parameters
##
@@ -495,7 +495,7 @@
<pre><code>## Simulating library sizes...</code></pre>
<pre><code>## Simulating gene means...</code></pre>
<pre><code>## Simulating BCV...</code></pre>
-<pre><code>## Simulating counts...</code></pre>
+<pre><code>## Simulating counts..</code></pre>
<pre><code>## Simulating dropout (if needed)...</code></pre>
<pre><code>## Done!</code></pre>
<div class="sourceCode" id="cb73"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb73-1" data-line-number="1">sim</a></code></pre></div>
@@ -513,54 +513,51 @@
<div class="sourceCode" id="cb75"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb75-1" data-line-number="1"><span class="co"># Access the counts</span></a>
<a class="sourceLine" id="cb75-2" data-line-number="2"><span class="kw">counts</span>(sim)[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
-## Gene1 13 0 1 46 7
-## Gene2 0 0 0 56 0
-## Gene3 2 511 0 80 5
-## Gene4 520 6672 34458 0 152
-## Gene5 20316 88 804 160 1420</code></pre>
+## Gene1 55 2 0 11 0
+## Gene2 1 2 0 0 0
+## Gene3 7 2 2 74 8
+## Gene4 0 69 6 0 114
+## Gene5 1 70 40 0 0</code></pre>
<div class="sourceCode" id="cb77"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb77-1" data-line-number="1"><span class="co"># Information about genes</span></a>
<a class="sourceLine" id="cb77-2" data-line-number="2"><span class="kw">head</span>(<span class="kw">rowData</span>(sim))</a></code></pre></div>
<pre><code>## DataFrame with 6 rows and 4 columns
-## Gene BaseGeneMean OutlierFactor GeneMean
-## <factor> <numeric> <numeric> <numeric>
-## Gene1 Gene1 4.70154390098128 1 4.70154390098128
-## Gene2 Gene2 45.2977291006656 1 45.2977291006656
-## Gene3 Gene3 16.739750293082 1 16.739750293082
-## Gene4 Gene4 859.114287247945 1 859.114287247945
-## Gene5 Gene5 833.536112103583 1 833.536112103583
-## Gene6 Gene6 115.240318940316 1 115.240318940316</code></pre>
+## Gene BaseGeneMean OutlierFactor GeneMean
+## <factor> <numeric> <numeric> <numeric>
+## 1 Gene1 76.9025430673341 1 76.9025430673341
+## 2 Gene2 11.5038956210654 1 11.5038956210654
+## 3 Gene3 9.5216589952532 1 9.5216589952532
+## 4 Gene4 740.124978536434 1 740.124978536434
+## 5 Gene5 71.5386607136642 1 71.5386607136642
+## 6 Gene6 1.06151313409539 1 1.06151313409539</code></pre>
<div class="sourceCode" id="cb79"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb79-1" data-line-number="1"><span class="co"># Information about cells</span></a>
<a class="sourceLine" id="cb79-2" data-line-number="2"><span class="kw">head</span>(<span class="kw">colData</span>(sim))</a></code></pre></div>
<pre><code>## DataFrame with 6 rows and 3 columns
## Cell Batch ExpLibSize
## <factor> <character> <numeric>
-## Cell1 Cell1 Batch1 616391.895194433
-## Cell2 Cell2 Batch1 466219.967307636
-## Cell3 Cell3 Batch1 534154.979473748
-## Cell4 Cell4 Batch1 394600.005164307
-## Cell5 Cell5 Batch1 185770.250355241
-## Cell6 Cell6 Batch1 342150.610770362</code></pre>
+## Cell1 Cell1 Batch1 510286.263476612
+## Cell2 Cell2 Batch1 1202024.11389745
+## Cell3 Cell3 Batch1 183908.161529651
+## Cell4 Cell4 Batch1 154585.938029774
+## Cell5 Cell5 Batch1 619536.71187027
+## Cell6 Cell6 Batch1 266676.834832325</code></pre>
<div class="sourceCode" id="cb81"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb81-1" data-line-number="1"><span class="co"># Gene by cell matrices</span></a>
<a class="sourceLine" id="cb81-2" data-line-number="2"><span class="kw">names</span>(<span class="kw">assays</span>(sim))</a></code></pre></div>
<pre><code>## [1] "BatchCellMeans" "BaseCellMeans" "BCV" "CellMeans"
## [5] "TrueCounts" "counts"</code></pre>
<div class="sourceCode" id="cb83"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb83-1" data-line-number="1"><span class="co"># Example of cell means matrix</span></a>
<a class="sourceLine" id="cb83-2" data-line-number="2"><span class="kw">assays</span>(sim)<span class="op">$</span>CellMeans[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
-<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
-## Gene1 1.050314e+01 5.692164e-03 7.494817e-02 40.7856290 4.5720652
-## Gene2 3.203912e-04 9.488383e-06 2.924749e-06 60.3712580 0.0513157
-## Gene3 2.661188e+00 5.066374e+02 2.532108e-10 90.8142373 4.3072914
-## Gene4 5.035784e+02 6.582460e+03 3.461912e+04 0.3223072 182.1801537
-## Gene5 2.049582e+04 8.280228e+01 7.914977e+02 140.3619760 1440.7795851</code></pre>
+<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
+## Gene1 5.333124e+01 2.598563 1.529988e-01 11.676286605 3.982157e-03
+## Gene2 7.665400e-01 7.586450 1.614969e-25 0.372529598 6.068763e-03
+## Gene3 6.121509e+00 1.784225 6.033250e+00 74.377980371 6.435478e+00
+## Gene4 8.789318e-06 69.991629 7.918106e+00 0.026909108 1.193434e+02
+## Gene5 8.940025e-02 94.814168 3.921096e+01 0.008752188 1.123261e-01</code></pre>
<p>An additional (big) advantage of outputting a <code>SingleCellExperiment</code> is that we get immediate access to other analysis packages, such as the plotting functions in <code>scater</code>. For example we can make a PCA plot:</p>
<div class="sourceCode" id="cb85"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb85-1" data-line-number="1"><span class="co"># Use scater to calculate logcounts</span></a>
<a class="sourceLine" id="cb85-2" data-line-number="2">sim <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim)</a></code></pre></div>
-<pre><code>## Warning: 'normalise' is deprecated.
-## Use 'normalize' instead.
-## See help("Deprecated")</code></pre>
<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
-<div class="sourceCode" id="cb88"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb88-1" data-line-number="1"><span class="co"># Plot PCA</span></a>
-<a class="sourceLine" id="cb88-2" data-line-number="2"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim)</a></code></pre></div>
+<div class="sourceCode" id="cb87"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb87-1" data-line-number="1"><span class="co"># Plot PCA</span></a>
+<a class="sourceLine" id="cb87-2" data-line-number="2"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim)</a></code></pre></div>
<p><img src="splatter_files/figure-html/pca-1.png" width="576" style="display: block; margin: auto;"></p>
<p>(<strong>NOTE:</strong> Your values and plots may look different as the simulation is random and produces different results each time it is run.)</p>
<p>For more details about the <code>SingleCellExperiment</code> object refer to the [vignette] <a href="https://bioconductor.org/packages/devel/bioc/vignettes/SingleCellExperiment/inst/doc/intro.html">SCE-vignette</a>. For information about what you can do with <code>scater</code> refer to the <code>scater</code> documentation and <a href="https://bioconductor.org/packages/release/bioc/vignettes/scater/inst/doc/vignette.html">vignette</a>.</p>
@@ -618,14 +615,11 @@
<a href="#simulating-groups" class="anchor"></a>Simulating groups</h2>
<p>So far we have only simulated a single population of cells but often we are interested in investigating a mixed population of cells and looking to see what cell types are present or what differences there are between them. Splatter is able to simulate these situations by changing the <code>method</code> argument Here we are going to simulate two groups, by specifying the <code>group.prob</code> parameter and setting the <code>method</code> parameter to <code>"groups"</code>:</p>
<p>(<strong>NOTE:</strong> We have also set the <code>verbose</code> argument to <code>FALSE</code> to stop Splatter printing progress messages.)</p>
-<div class="sourceCode" id="cb89"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb89-1" data-line-number="1">sim.groups <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">group.prob =</span> <span class="kw">c</span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>), <span class="dt">method =</span> <span class="st">"groups"</span>,</a>
-<a class="sourceLine" id="cb89-2" data-line-number="2"> <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb89-3" data-line-number="3">sim.groups <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.groups)</a></code></pre></div>
-<pre><code>## Warning: 'normalise' is deprecated.
-## Use 'normalize' instead.
-## See help("Deprecated")</code></pre>
+<div class="sourceCode" id="cb88"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb88-1" data-line-number="1">sim.groups <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">group.prob =</span> <span class="kw">c</span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>), <span class="dt">method =</span> <span class="st">"groups"</span>,</a>
+<a class="sourceLine" id="cb88-2" data-line-number="2"> <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb88-3" data-line-number="3">sim.groups <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.groups)</a></code></pre></div>
<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
-<div class="sourceCode" id="cb92"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb92-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.groups, <span class="dt">colour_by =</span> <span class="st">"Group"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb90"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb90-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.groups, <span class="dt">colour_by =</span> <span class="st">"Group"</span>)</a></code></pre></div>
<p><img src="splatter_files/figure-html/groups-1.png" width="576" style="display: block; margin: auto;"></p>
<p>As we have set both the group probabilites to 0.5 we should get approximately equal numbers of cells in each group (around 50 in this case). If we wanted uneven groups we could set <code>group.prob</code> to any set of probabilites that sum to 1.</p>
</div>
@@ -633,13 +627,10 @@
<h2 class="hasAnchor">
<a href="#simulating-paths" class="anchor"></a>Simulating paths</h2>
<p>The other situation that is often of interest is a differentiation process where one cell type is changing into another. Splatter approximates this process by simulating a series of steps between two groups and randomly assigning each cell to a step. We can create this kind of simulation using the <code>"paths"</code> method.</p>
-<div class="sourceCode" id="cb93"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb93-1" data-line-number="1">sim.paths <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">method =</span> <span class="st">"paths"</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb93-2" data-line-number="2">sim.paths <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.paths)</a></code></pre></div>
-<pre><code>## Warning: 'normalise' is deprecated.
-## Use 'normalize' instead.
-## See help("Deprecated")</code></pre>
+<div class="sourceCode" id="cb91"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb91-1" data-line-number="1">sim.paths <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">method =</span> <span class="st">"paths"</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb91-2" data-line-number="2">sim.paths <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.paths)</a></code></pre></div>
<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
-<div class="sourceCode" id="cb96"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb96-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.paths, <span class="dt">colour_by =</span> <span class="st">"Step"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb93"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb93-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.paths, <span class="dt">colour_by =</span> <span class="st">"Step"</span>)</a></code></pre></div>
<p><img src="splatter_files/figure-html/paths-1.png" width="576" style="display: block; margin: auto;"></p>
<p>Here the colours represent the “step†of each cell or how far along the differentiation path it is. We can see that the cells with dark colours are more similar to the originating cell type and the light coloured cells are closer to the final, differentiated, cell type. By setting additional parameters it is possible to simulate more complex process (for example multiple mature cell types from a single progenitor).</p>
</div>
@@ -647,23 +638,17 @@
<h2 class="hasAnchor">
<a href="#batch-effects" class="anchor"></a>Batch effects</h2>
<p>Another factor that is important in the analysis of any sequencing experiment are batch effects, technical variation that is common to a set of samples processed at the same time. We apply batch effects by telling Splatter how many cells are in each batch:</p>
-<div class="sourceCode" id="cb97"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb97-1" data-line-number="1">sim.batches <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">batchCells =</span> <span class="kw">c</span>(<span class="dv">50</span>, <span class="dv">50</span>), <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb97-2" data-line-number="2">sim.batches <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.batches)</a></code></pre></div>
-<pre><code>## Warning: 'normalise' is deprecated.
-## Use 'normalize' instead.
-## See help("Deprecated")</code></pre>
+<div class="sourceCode" id="cb94"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb94-1" data-line-number="1">sim.batches <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">batchCells =</span> <span class="kw">c</span>(<span class="dv">50</span>, <span class="dv">50</span>), <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb94-2" data-line-number="2">sim.batches <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.batches)</a></code></pre></div>
<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
-<div class="sourceCode" id="cb100"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb100-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.batches, <span class="dt">colour_by =</span> <span class="st">"Batch"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb96"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb96-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.batches, <span class="dt">colour_by =</span> <span class="st">"Batch"</span>)</a></code></pre></div>
<p><img src="splatter_files/figure-html/batches-1.png" width="576" style="display: block; margin: auto;"></p>
<p>This looks at lot like when we simulated groups and that is because the process is very similar. The difference is that batch effects are applied to all genes, not just those that are differentially expressed, and the effects are usually smaller. By combining groups and batches we can simulate both unwanted variation that we aren’t interested in (batch) and the wanted variation we are looking for (group):</p>
-<div class="sourceCode" id="cb101"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb101-1" data-line-number="1">sim.groups <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">batchCells =</span> <span class="kw">c</span>(<span class="dv">50</span>, <span class="dv">50</span>), <span class="dt">group.prob =</span> <span class="kw">c</span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>),</a>
-<a class="sourceLine" id="cb101-2" data-line-number="2"> <span class="dt">method =</span> <span class="st">"groups"</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb101-3" data-line-number="3">sim.groups <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.groups)</a></code></pre></div>
-<pre><code>## Warning: 'normalise' is deprecated.
-## Use 'normalize' instead.
-## See help("Deprecated")</code></pre>
+<div class="sourceCode" id="cb97"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb97-1" data-line-number="1">sim.groups <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">batchCells =</span> <span class="kw">c</span>(<span class="dv">50</span>, <span class="dv">50</span>), <span class="dt">group.prob =</span> <span class="kw">c</span>(<span class="fl">0.5</span>, <span class="fl">0.5</span>),</a>
+<a class="sourceLine" id="cb97-2" data-line-number="2"> <span class="dt">method =</span> <span class="st">"groups"</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb97-3" data-line-number="3">sim.groups <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/normalize">normalise</a></span>(sim.groups)</a></code></pre></div>
<pre><code>## Warning in .local(object, ...): using library sizes as size factors</code></pre>
-<div class="sourceCode" id="cb104"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb104-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.groups, <span class="dt">shape_by =</span> <span class="st">"Batch"</span>, <span class="dt">colour_by =</span> <span class="st">"Group"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb99"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb99-1" data-line-number="1"><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/plot_reddim">plotPCA</a></span>(sim.groups, <span class="dt">shape_by =</span> <span class="st">"Batch"</span>, <span class="dt">colour_by =</span> <span class="st">"Group"</span>)</a></code></pre></div>
<p><img src="splatter_files/figure-html/batch-groups-1.png" width="576" style="display: block; margin: auto;"></p>
<p>Here we see that the effects of the group (first component) are stronger than the batch effects (second component) but by adjusting the parameters we could made the batch effects dominate.</p>
</div>
@@ -677,7 +662,7 @@
<h1 class="hasAnchor">
<a href="#other-simulations" class="anchor"></a>Other simulations</h1>
<p>As well as it’s own Splat simulation method the Splatter package contains implementations of other single-cell RNA-seq simulations that have been published or wrappers around simulations included in other packages. To see all the available simulations run the <code><a href="../reference/listSims.html">listSims()</a></code> function:</p>
-<div class="sourceCode" id="cb105"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb105-1" data-line-number="1"><span class="kw"><a href="../reference/listSims.html">listSims</a></span>()</a></code></pre></div>
+<div class="sourceCode" id="cb100"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb100-1" data-line-number="1"><span class="kw"><a href="../reference/listSims.html">listSims</a></span>()</a></code></pre></div>
<pre><code>## Splatter currently contains 13 simulations
##
## Splat (splat)
@@ -732,7 +717,7 @@
## DOI: 10.1093/nar/gkx1113 GitHub: cran/SparseDC
## The SparseDC simulation simulates a set of clusters across two conditions, where some clusters may be present in only one condition.</code></pre>
<p>(or more conveniently for the vignette as a table)</p>
-<div class="sourceCode" id="cb107"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb107-1" data-line-number="1">knitr<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/knitr/topics/kable">kable</a></span>(<span class="kw"><a href="../reference/listSims.html">listSims</a></span>(<span class="dt">print =</span> <span class="ot">FALSE</span>))</a></code></pre></div>
+<div class="sourceCode" id="cb102"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb102-1" data-line-number="1">knitr<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/knitr/topics/kable">kable</a></span>(<span class="kw"><a href="../reference/listSims.html">listSims</a></span>(<span class="dt">print =</span> <span class="ot">FALSE</span>))</a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="left">Name</th>
@@ -841,60 +826,67 @@
<h1 class="hasAnchor">
<a href="#other-expression-values" class="anchor"></a>Other expression values</h1>
<p>Splatter is designed to simulate count data but some analysis methods expect other expression values, particularly length-normalised values such as TPM or FPKM. The <code>scater</code> package has functions for adding these values to a <code>SingleCellExperiment</code> object but they require a length for each gene. The <code>addGeneLengths</code> function can be used to simulate these lengths:</p>
-<div class="sourceCode" id="cb108"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb108-1" data-line-number="1">sim <-<span class="st"> </span><span class="kw"><a href="../reference/simpleSimulate.html">simpleSimulate</a></span>(<span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb108-2" data-line-number="2">sim <-<span class="st"> </span><span class="kw"><a href="../reference/addGeneLengths.html">addGeneLengths</a></span>(sim)</a>
-<a class="sourceLine" id="cb108-3" data-line-number="3"><span class="kw">head</span>(<span class="kw">rowData</span>(sim))</a></code></pre></div>
+<div class="sourceCode" id="cb103"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb103-1" data-line-number="1">sim <-<span class="st"> </span><span class="kw"><a href="../reference/simpleSimulate.html">simpleSimulate</a></span>(<span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb103-2" data-line-number="2">sim <-<span class="st"> </span><span class="kw"><a href="../reference/addGeneLengths.html">addGeneLengths</a></span>(sim)</a>
+<a class="sourceLine" id="cb103-3" data-line-number="3"><span class="kw">head</span>(<span class="kw">rowData</span>(sim))</a></code></pre></div>
<pre><code>## DataFrame with 6 rows and 3 columns
-## Gene GeneMean Length
-## <factor> <numeric> <numeric>
-## Gene1 Gene1 1.42337872195248 5214
-## Gene2 Gene2 0.0522297815343736 1028
-## Gene3 Gene3 0.9405738811201 8949
-## Gene4 Gene4 0.634058823619169 6227
-## Gene5 Gene5 0.02180661228227 4138
-## Gene6 Gene6 0.000761752736734951 7339</code></pre>
+## Gene GeneMean Length
+## <factor> <numeric> <numeric>
+## 1 Gene1 0.0489642776646331 1937
+## 2 Gene2 3.20462567086451 2196
+## 3 Gene3 0.364784855489904 9883
+## 4 Gene4 0.110583350422224 1810
+## 5 Gene5 0.661617770742839 1177
+## 6 Gene6 0.101683292027918 2012</code></pre>
<p>We can then use <code>scater</code> to calculate TPM:</p>
-<div class="sourceCode" id="cb110"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb110-1" data-line-number="1"><span class="kw">tpm</span>(sim) <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/calculateTPM">calculateTPM</a></span>(sim, <span class="kw">rowData</span>(sim)<span class="op">$</span>Length)</a>
-<a class="sourceLine" id="cb110-2" data-line-number="2"><span class="kw">tpm</span>(sim)[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
-<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
-## Gene1 30.57200 92.71564 92.91733 0 0
-## Gene2 0.00000 0.00000 157.09174 0 0
-## Gene3 35.62463 18.00646 18.04563 0 0
-## Gene4 0.00000 0.00000 25.93389 0 0
-## Gene5 0.00000 0.00000 0.00000 0 0</code></pre>
+<div class="sourceCode" id="cb105"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb105-1" data-line-number="1"><span class="kw">tpm</span>(sim) <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/scater/topics/calculateTPM">calculateTPM</a></span>(sim, <span class="kw">rowData</span>(sim)<span class="op">$</span>Length)</a>
+<a class="sourceLine" id="cb105-2" data-line-number="2"><span class="kw">tpm</span>(sim)[<span class="dv">1</span><span class="op">:</span><span class="dv">5</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">5</span>]</a></code></pre></div>
+<pre><code>## Cell1 Cell2 Cell3 Cell4 Cell5
+## Gene1 0.0000000 0.000000000 0.00000000 0.000000000 0.000000000
+## Gene2 0.2338332 0.033654084 0.09984799 0.000000000 0.066541011
+## Gene3 0.0000000 0.007477929 0.00000000 0.007379757 0.007392698
+## Gene4 0.0000000 0.000000000 0.04038051 0.000000000 0.000000000
+## Gene5 0.0000000 0.062790457 0.06209748 0.247864539 0.000000000</code></pre>
<p>The default method used by <code>addGeneLengths</code> to simulate lengths is to generate values from a log-normal distribution which are then rounded to give an integer length. The parameters for this distribution are based on human protein coding genes but can be adjusted if needed (for example for other species). Alternatively lengths can be sampled from a provided vector (see <code><a href="../reference/addGeneLengths.html">?addGeneLengths</a></code> for details and an example).</p>
</div>
<div id="comparing-simulations-and-real-data" class="section level1">
<h1 class="hasAnchor">
<a href="#comparing-simulations-and-real-data" class="anchor"></a>Comparing simulations and real data</h1>
<p>One thing you might like to do after simulating data is to compare it to a real dataset, or compare simulations with different parameters or models. Splatter provides a function <code>compareSCEs</code> that aims to make these comparisons easier. As the name suggests this function takes a list of <code>SingleCellExperiment</code> objects, combines the datasets and produces some plots comparing them. Let’s make two small simulations and see how they compare.</p>
-<div class="sourceCode" id="cb112"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb112-1" data-line-number="1">sim1 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">nGenes =</span> <span class="dv">1000</span>, <span class="dt">batchCells =</span> <span class="dv">20</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb112-2" data-line-number="2">sim2 <-<span class="st"> </span><span class="kw"><a href="../reference/simpleSimulate.html">simpleSimulate</a></span>(<span class="dt">nGenes =</span> <span class="dv">1000</span>, <span class="dt">nCells =</span> <span class="dv">20</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb112-3" data-line-number="3">comparison <-<span class="st"> </span><span class="kw"><a href="../reference/compareSCEs.html">compareSCEs</a></span>(<span class="kw">list</span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2))</a>
-<a class="sourceLine" id="cb112-4" data-line-number="4"></a>
-<a class="sourceLine" id="cb112-5" data-line-number="5"><span class="kw">names</span>(comparison)</a></code></pre></div>
+<div class="sourceCode" id="cb107"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb107-1" data-line-number="1">sim1 <-<span class="st"> </span><span class="kw"><a href="../reference/splatSimulate.html">splatSimulate</a></span>(<span class="dt">nGenes =</span> <span class="dv">1000</span>, <span class="dt">batchCells =</span> <span class="dv">20</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb107-2" data-line-number="2">sim2 <-<span class="st"> </span><span class="kw"><a href="../reference/simpleSimulate.html">simpleSimulate</a></span>(<span class="dt">nGenes =</span> <span class="dv">1000</span>, <span class="dt">nCells =</span> <span class="dv">20</span>, <span class="dt">verbose =</span> <span class="ot">FALSE</span>)</a>
+<a class="sourceLine" id="cb107-3" data-line-number="3">comparison <-<span class="st"> </span><span class="kw"><a href="../reference/compareSCEs.html">compareSCEs</a></span>(<span class="kw">list</span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2))</a></code></pre></div>
+<pre><code>## Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.
+## Old names are currently maintained for back-compatibility, but may be removed in future releases.
+## Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.
+## Old names are currently maintained for back-compatibility, but may be removed in future releases.</code></pre>
+<div class="sourceCode" id="cb109"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb109-1" data-line-number="1"><span class="kw">names</span>(comparison)</a></code></pre></div>
<pre><code>## [1] "FeatureData" "PhenoData" "Plots"</code></pre>
-<div class="sourceCode" id="cb114"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb114-1" data-line-number="1"><span class="kw">names</span>(comparison<span class="op">$</span>Plots)</a></code></pre></div>
+<div class="sourceCode" id="cb111"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb111-1" data-line-number="1"><span class="kw">names</span>(comparison<span class="op">$</span>Plots)</a></code></pre></div>
<pre><code>## [1] "Means" "Variances" "MeanVar" "LibrarySizes"
## [5] "ZerosGene" "ZerosCell" "MeanZeros"</code></pre>
<p>The returned list has three items. The first two are the combined datasets by gene (<code>FeatureData</code>) and by cell (<code>PhenoData</code>) and the third contains some comparison plots (produced using <code>ggplot2</code>), for example a plot of the distribution of means:</p>
-<div class="sourceCode" id="cb116"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb116-1" data-line-number="1">comparison<span class="op">$</span>Plots<span class="op">$</span>Means</a></code></pre></div>
+<div class="sourceCode" id="cb113"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb113-1" data-line-number="1">comparison<span class="op">$</span>Plots<span class="op">$</span>Means</a></code></pre></div>
<p><img src="splatter_files/figure-html/comparison-means-1.png" width="576" style="display: block; margin: auto;"></p>
<p>These are only a few of the plots you might want to consider but it should be easy to make more using the returned data. For example, we could plot the number of expressed genes against the library size:</p>
-<div class="sourceCode" id="cb117"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb117-1" data-line-number="1"><span class="kw">library</span>(<span class="st">"ggplot2"</span>)</a>
-<a class="sourceLine" id="cb117-2" data-line-number="2"><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>(comparison<span class="op">$</span>PhenoData,</a>
-<a class="sourceLine" id="cb117-3" data-line-number="3"> <span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(<span class="dt">x =</span> total_counts, <span class="dt">y =</span> total_features_by_counts, <span class="dt">colour =</span> Dataset)) <span class="op">+</span></a>
-<a class="sourceLine" id="cb117-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_point">geom_point</a></span>()</a></code></pre></div>
+<div class="sourceCode" id="cb114"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb114-1" data-line-number="1"><span class="kw">library</span>(<span class="st">"ggplot2"</span>)</a>
+<a class="sourceLine" id="cb114-2" data-line-number="2"><span class="kw"><a href="ggplot2.tidyverse.org/reference/ggplot.html">ggplot</a></span>(comparison<span class="op">$</span>PhenoData,</a>
+<a class="sourceLine" id="cb114-3" data-line-number="3"> <span class="kw"><a href="ggplot2.tidyverse.org/reference/aes.html">aes</a></span>(<span class="dt">x =</span> total_counts, <span class="dt">y =</span> total_features_by_counts, <span class="dt">colour =</span> Dataset)) <span class="op">+</span></a>
+<a class="sourceLine" id="cb114-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="ggplot2.tidyverse.org/reference/geom_point.html">geom_point</a></span>()</a></code></pre></div>
<p><img src="splatter_files/figure-html/comparison-libsize-features-1.png" width="576" style="display: block; margin: auto;"></p>
<div id="comparing-differences" class="section level2">
<h2 class="hasAnchor">
<a href="#comparing-differences" class="anchor"></a>Comparing differences</h2>
<p>Sometimes instead of visually comparing datasets it may be more interesting to look at the differences between them. We can do this using the <code>diffSCEs</code> function. Similar to <code>compareSCEs</code> this function takes a list of <code>SingleCellExperiment</code> objects but now we also specify one to be a reference. A series of similar plots are returned but instead of showing the overall distributions they demonstrate differences from the reference.</p>
-<div class="sourceCode" id="cb118"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb118-1" data-line-number="1">difference <-<span class="st"> </span><span class="kw"><a href="../reference/diffSCEs.html">diffSCEs</a></span>(<span class="kw">list</span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2), <span class="dt">ref =</span> <span class="st">"Simple"</span>)</a>
-<a class="sourceLine" id="cb118-2" data-line-number="2">difference<span class="op">$</span>Plots<span class="op">$</span>Means</a></code></pre></div>
+<div class="sourceCode" id="cb115"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb115-1" data-line-number="1">difference <-<span class="st"> </span><span class="kw"><a href="../reference/diffSCEs.html">diffSCEs</a></span>(<span class="kw">list</span>(<span class="dt">Splat =</span> sim1, <span class="dt">Simple =</span> sim2), <span class="dt">ref =</span> <span class="st">"Simple"</span>)</a></code></pre></div>
+<pre><code>## Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.
+## Old names are currently maintained for back-compatibility, but may be removed in future releases.
+## Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.
+## Old names are currently maintained for back-compatibility, but may be removed in future releases.</code></pre>
+<div class="sourceCode" id="cb117"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb117-1" data-line-number="1">difference<span class="op">$</span>Plots<span class="op">$</span>Means</a></code></pre></div>
<p><img src="splatter_files/figure-html/difference-1.png" width="576" style="display: block; margin: auto;"></p>
<p>We also get a series of Quantile-Quantile plot that can be used to compare distributions.</p>
-<div class="sourceCode" id="cb119"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb119-1" data-line-number="1">difference<span class="op">$</span>QQPlots<span class="op">$</span>Means</a></code></pre></div>
+<div class="sourceCode" id="cb118"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb118-1" data-line-number="1">difference<span class="op">$</span>QQPlots<span class="op">$</span>Means</a></code></pre></div>
<p><img src="splatter_files/figure-html/difference-qq-1.png" width="576" style="display: block; margin: auto;"></p>
</div>
<div id="making-panels" class="section level2">
@@ -902,22 +894,22 @@
<a href="#making-panels" class="anchor"></a>Making panels</h2>
<p>Each of these comparisons makes several plots which can be a lot to look at. To make this easier, or to produce figures for publications, you can make use of the functions <code>makeCompPanel</code>, <code>makeDiffPanel</code> and <code>makeOverallPanel</code>.</p>
<p>These functions combine the plots into a single panel using the <code>cowplot</code> package. The panels can be quite large and hard to view (for example in RStudio’s plot viewer) so it can be better to output the panels and view them separately. Luckily <code>cowplot</code> provides a convenient function for saving the images. Here are some suggested parameters for outputting each of the panels:</p>
-<div class="sourceCode" id="cb120"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb120-1" data-line-number="1"><span class="co"># This code is just an example and is not run</span></a>
-<a class="sourceLine" id="cb120-2" data-line-number="2">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeCompPanel.html">makeCompPanel</a></span>(comparison)</a>
-<a class="sourceLine" id="cb120-3" data-line-number="3">cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"comp_panel.png"</span>, panel, <span class="dt">nrow =</span> <span class="dv">4</span>, <span class="dt">ncol =</span> <span class="dv">3</span>)</a>
-<a class="sourceLine" id="cb120-4" data-line-number="4"></a>
-<a class="sourceLine" id="cb120-5" data-line-number="5">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeDiffPanel.html">makeDiffPanel</a></span>(difference)</a>
-<a class="sourceLine" id="cb120-6" data-line-number="6">cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"diff_panel.png"</span>, panel, <span class="dt">nrow =</span> <span class="dv">3</span>, <span class="dt">ncol =</span> <span class="dv">5</span>)</a>
-<a class="sourceLine" id="cb120-7" data-line-number="7"></a>
-<a class="sourceLine" id="cb120-8" data-line-number="8">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeOverallPanel.html">makeOverallPanel</a></span>(comparison, difference)</a>
-<a class="sourceLine" id="cb120-9" data-line-number="9">cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"overall_panel.png"</span>, panel, <span class="dt">ncol =</span> <span class="dv">4</span>, <span class="dt">nrow =</span> <span class="dv">7</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb119"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb119-1" data-line-number="1"><span class="co"># This code is just an example and is not run</span></a>
+<a class="sourceLine" id="cb119-2" data-line-number="2">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeCompPanel.html">makeCompPanel</a></span>(comparison)</a>
+<a class="sourceLine" id="cb119-3" data-line-number="3">cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"comp_panel.png"</span>, panel, <span class="dt">nrow =</span> <span class="dv">4</span>, <span class="dt">ncol =</span> <span class="dv">3</span>)</a>
+<a class="sourceLine" id="cb119-4" data-line-number="4"></a>
+<a class="sourceLine" id="cb119-5" data-line-number="5">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeDiffPanel.html">makeDiffPanel</a></span>(difference)</a>
+<a class="sourceLine" id="cb119-6" data-line-number="6">cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"diff_panel.png"</span>, panel, <span class="dt">nrow =</span> <span class="dv">3</span>, <span class="dt">ncol =</span> <span class="dv">5</span>)</a>
+<a class="sourceLine" id="cb119-7" data-line-number="7"></a>
+<a class="sourceLine" id="cb119-8" data-line-number="8">panel <-<span class="st"> </span><span class="kw"><a href="../reference/makeOverallPanel.html">makeOverallPanel</a></span>(comparison, difference)</a>
+<a class="sourceLine" id="cb119-9" data-line-number="9">cowplot<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/cowplot/topics/save_plot">save_plot</a></span>(<span class="st">"overall_panel.png"</span>, panel, <span class="dt">ncol =</span> <span class="dv">4</span>, <span class="dt">nrow =</span> <span class="dv">7</span>)</a></code></pre></div>
</div>
</div>
<div id="citing-splatter" class="section level1">
<h1 class="hasAnchor">
<a href="#citing-splatter" class="anchor"></a>Citing Splatter</h1>
<p>If you use Splatter in your work please cite our paper:</p>
-<div class="sourceCode" id="cb121"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb121-1" data-line-number="1"><span class="kw">citation</span>(<span class="st">"splatter"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb120"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb120-1" data-line-number="1"><span class="kw">citation</span>(<span class="st">"splatter"</span>)</a></code></pre></div>
<pre><code>##
## Zappia L, Phipson B, Oshlack A. Splatter: Simulation of
## single-cell RNA sequencing data. Genome Biology. 2017;
@@ -937,7 +929,7 @@
<div id="session-information" class="section level1 unnumbered">
<h1 class="hasAnchor">
<a href="#session-information" class="anchor"></a>Session information</h1>
-<div class="sourceCode" id="cb123"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb123-1" data-line-number="1"><span class="kw">sessionInfo</span>()</a></code></pre></div>
+<div class="sourceCode" id="cb122"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb122-1" data-line-number="1"><span class="kw">sessionInfo</span>()</a></code></pre></div>
<pre><code>## R version 3.5.1 (2018-07-02)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Sierra 10.12.6
@@ -954,56 +946,58 @@
## [8] methods base
##
## other attached packages:
-## [1] scater_1.9.23 ggplot2_3.0.0.9000
-## [3] splatter_1.5.7 SingleCellExperiment_1.3.11
-## [5] SummarizedExperiment_1.11.6 DelayedArray_0.7.48
-## [7] BiocParallel_1.15.15 matrixStats_0.54.0
-## [9] Biobase_2.41.2 GenomicRanges_1.33.14
-## [11] GenomeInfoDb_1.17.4 IRanges_2.15.18
-## [13] S4Vectors_0.19.22 BiocGenerics_0.27.1
-## [15] BiocStyle_2.9.6
+## [1] scater_1.8.4 ggplot2_3.0.0
+## [3] splatter_1.4.3 SingleCellExperiment_1.2.0
+## [5] SummarizedExperiment_1.10.1 DelayedArray_0.6.5
+## [7] BiocParallel_1.14.2 matrixStats_0.54.0
+## [9] Biobase_2.40.0 GenomicRanges_1.32.6
+## [11] GenomeInfoDb_1.16.0 IRanges_2.14.11
+## [13] S4Vectors_0.18.3 BiocGenerics_0.26.0
+## [15] BiocStyle_2.8.2
##
## loaded via a namespace (and not attached):
-## [1] bitops_1.0-6 fs_1.2.6
-## [3] rprojroot_1.3-2 tools_3.5.1
-## [5] backports_1.1.2 R6_2.3.0
-## [7] HDF5Array_1.9.19 vipor_0.4.5
-## [9] lazyeval_0.2.1 colorspace_1.3-2
-## [11] npsurv_0.4-0 withr_2.1.2
-## [13] sp_1.3-1 tidyselect_0.2.5
-## [15] gridExtra_2.3 compiler_3.5.1
-## [17] xml2_1.2.0 desc_1.2.0
-## [19] labeling_0.3 bookdown_0.7
-## [21] scales_1.0.0 checkmate_1.8.5
-## [23] pkgdown_1.1.0 commonmark_1.6
-## [25] stringr_1.3.1 digest_0.6.18
-## [27] rmarkdown_1.10 XVector_0.21.4
-## [29] pkgconfig_2.0.2 htmltools_0.3.6
-## [31] akima_0.6-2 limma_3.37.10
-## [33] highr_0.7 rlang_0.2.2
-## [35] rstudioapi_0.8 DelayedMatrixStats_1.3.11
-## [37] bindr_0.1.1 dplyr_0.7.7
-## [39] RCurl_1.95-4.11 magrittr_1.5
-## [41] GenomeInfoDbData_1.2.0 Matrix_1.2-14
-## [43] Rcpp_0.12.19 ggbeeswarm_0.6.0
-## [45] munsell_0.5.0 Rhdf5lib_1.3.3
-## [47] viridis_0.5.1 stringi_1.2.4
-## [49] yaml_2.2.0 edgeR_3.23.5
-## [51] MASS_7.3-51 zlibbioc_1.27.0
-## [53] rhdf5_2.25.11 plyr_1.8.4
-## [55] grid_3.5.1 crayon_1.3.4
-## [57] lattice_0.20-35 cowplot_0.9.3
-## [59] splines_3.5.1 locfit_1.5-9.1
-## [61] knitr_1.20 pillar_1.3.0
-## [63] reshape2_1.4.3 glue_1.3.0
-## [65] evaluate_0.12 lsei_1.2-0
-## [67] BiocManager_1.30.3 gtable_0.2.0
-## [69] purrr_0.2.5 assertthat_0.2.0
-## [71] xfun_0.3 roxygen2_6.1.0
-## [73] survival_2.42-6 viridisLite_0.3.0
-## [75] tibble_1.4.2 beeswarm_0.2.3
-## [77] memoise_1.1.0 bindrcpp_0.2.2
-## [79] fitdistrplus_1.0-11</code></pre>
+## [1] bitops_1.0-6 fs_1.2.6
+## [3] rprojroot_1.3-2 tools_3.5.1
+## [5] backports_1.1.2 R6_2.2.2
+## [7] vipor_0.4.5 lazyeval_0.2.1
+## [9] colorspace_1.3-2 sp_1.3-1
+## [11] withr_2.1.2 tidyselect_0.2.4
+## [13] gridExtra_2.3 compiler_3.5.1
+## [15] xml2_1.2.0 desc_1.2.0
+## [17] labeling_0.3 bookdown_0.7
+## [19] scales_1.0.0 checkmate_1.8.6
+## [21] pkgdown_1.1.0 commonmark_1.5
+## [23] stringr_1.3.1 digest_0.6.16
+## [25] rmarkdown_1.10 XVector_0.20.0
+## [27] pkgconfig_2.0.2 htmltools_0.3.6
+## [29] akima_0.6-2 highr_0.7
+## [31] limma_3.36.3 rlang_0.2.2
+## [33] shiny_1.1.0 DelayedMatrixStats_1.2.0
+## [35] bindr_0.1.1 dplyr_0.7.6
+## [37] RCurl_1.95-4.11 magrittr_1.5
+## [39] GenomeInfoDbData_1.1.0 Matrix_1.2-14
+## [41] Rcpp_0.12.18 ggbeeswarm_0.6.0
+## [43] munsell_0.5.0 Rhdf5lib_1.2.1
+## [45] viridis_0.5.1 stringi_1.2.4
+## [47] yaml_2.2.0 edgeR_3.22.3
+## [49] MASS_7.3-51 zlibbioc_1.26.0
+## [51] rhdf5_2.24.0 plyr_1.8.4
+## [53] grid_3.5.1 promises_1.0.1
+## [55] shinydashboard_0.7.0 crayon_1.3.4
+## [57] lattice_0.20-35 cowplot_0.9.3
+## [59] splines_3.5.1 locfit_1.5-9.1
+## [61] knitr_1.20 pillar_1.3.0
+## [63] rjson_0.2.20 reshape2_1.4.3
+## [65] glue_1.3.0 evaluate_0.11
+## [67] data.table_1.11.4 httpuv_1.4.5
+## [69] gtable_0.2.0 purrr_0.2.5
+## [71] assertthat_0.2.0 xfun_0.3
+## [73] mime_0.5 xtable_1.8-3
+## [75] roxygen2_6.1.0 later_0.7.4
+## [77] survival_2.42-6 viridisLite_0.3.0
+## [79] tibble_1.4.2 beeswarm_0.2.3
+## [81] memoise_1.1.0 tximport_1.8.0
+## [83] bindrcpp_0.2.2 fitdistrplus_1.0-9</code></pre>
</div>
</div>
diff --git a/docs/articles/splatter_files/figure-html/batch-groups-1.png b/docs/articles/splatter_files/figure-html/batch-groups-1.png
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diff --git a/docs/articles/splatter_files/figure-html/difference-qq-1.png b/docs/articles/splatter_files/figure-html/difference-qq-1.png
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diff --git a/docs/articles/splatter_files/figure-html/groups-1.png b/docs/articles/splatter_files/figure-html/groups-1.png
index 8dc31a6b28680f366df2395d31c122ee5905444a..c985872ba0a762ef0a11eceae64ac608e37f59e3 100644
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diff --git a/docs/articles/splatter_files/figure-html/paths-1.png b/docs/articles/splatter_files/figure-html/paths-1.png
index c7f96ee197e55f4ad89051caadc1708992db779a..d13dc6196bd0ba01be8f4539abc0074daa75b87a 100644
Binary files a/docs/articles/splatter_files/figure-html/paths-1.png and b/docs/articles/splatter_files/figure-html/paths-1.png differ
diff --git a/docs/articles/splatter_files/figure-html/pca-1.png b/docs/articles/splatter_files/figure-html/pca-1.png
index 03dc80ab05a89c2f913dbf7db7ab210521d562c0..bf92e106b921a619c42b1a9a18a891ff0291ded4 100644
Binary files a/docs/articles/splatter_files/figure-html/pca-1.png and b/docs/articles/splatter_files/figure-html/pca-1.png differ
diff --git a/docs/authors.html b/docs/authors.html
index 39426bfbc6f34a29a45cf7b41d0ee78acc1e15cc..ec616f5196a982a81929e21695cde7952766d0a2 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -70,7 +70,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/index.html b/docs/index.html
index de1e28602c6c9f59107e8548fa1077c77a175042..2bcae7ff6f15e153b89b6361a7d181bc62f48a4e 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -40,7 +40,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/news/index.html b/docs/news/index.html
index c3d03a4c582a57cc08716a641be7cfce0309cb2a..7d224facb51138dea7c54f295858d39cb105c917 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -70,7 +70,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
@@ -116,28 +116,32 @@
<small>Source: <a href='https://github.com/Oshlack/splatter/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
- <div id="version-1-5-8-2018-10-22" class="section level2">
+ <div id="version-1-6-0-2018-11-01" class="section level1">
+<h1 class="page-header">
+<a href="#version-1-6-0-2018-11-01" class="anchor"></a>Version 1.6.0 (2018-11-01)</h1>
+<p>Bioconductor 3.8 release</p>
+<div id="version-1-5-8-2018-10-22" class="section level2">
<h2 class="hasAnchor">
<a href="#version-1-5-8-2018-10-22" class="anchor"></a>Version 1.5.8 (2018-10-22)</h2>
<ul>
<li>Add WithSpikes argument when calling BASiCS::BASiCS_MCMC()</li>
</ul>
</div>
- <div id="version-1-5-7-2018-10-03" class="section level2">
+<div id="version-1-5-7-2018-10-03" class="section level2">
<h2 class="hasAnchor">
<a href="#version-1-5-7-2018-10-03" class="anchor"></a>Version 1.5.7 (2018-10-03)</h2>
<ul>
<li>Fix BASiCSEstimate tests</li>
</ul>
</div>
- <div id="version-1-5-4-2018-08-30" class="section level2">
+<div id="version-1-5-4-2018-08-30" class="section level2">
<h2 class="hasAnchor">
<a href="#version-1-5-4-2018-08-30" class="anchor"></a>Version 1.5.4 (2018-08-30)</h2>
<ul>
<li>Fix installation instructions</li>
</ul>
</div>
- <div id="version-1-5-3-2018-08-20" class="section level2">
+<div id="version-1-5-3-2018-08-20" class="section level2">
<h2 class="hasAnchor">
<a href="#version-1-5-3-2018-08-20" class="anchor"></a>Version 1.5.3 (2018-08-20)</h2>
<ul>
@@ -152,7 +156,7 @@
</ul>
</div>
</div>
- <div id="version-1-5-2-2018-08-16" class="section level2">
+<div id="version-1-5-2-2018-08-16" class="section level2">
<h2 class="hasAnchor">
<a href="#version-1-5-2-2018-08-16" class="anchor"></a>Version 1.5.2 (2018-08-16)</h2>
<ul>
@@ -162,7 +166,7 @@
<li>Add suggested package checks to tests</li>
</ul>
</div>
- <div id="version-1-5-1-2018-06-12" class="section level2">
+<div id="version-1-5-1-2018-06-12" class="section level2">
<h2 class="hasAnchor">
<a href="#version-1-5-1-2018-06-12" class="anchor"></a>Version 1.5.1 (2018-06-12)</h2>
<ul>
@@ -171,21 +175,21 @@
<li>Sample library sizes for normality testing if > 5000 cells</li>
</ul>
</div>
- <div id="version-1-5-0-2018-05-02" class="section level2">
+<div id="version-1-5-0-2018-05-02" class="section level2">
<h2 class="hasAnchor">
<a href="#version-1-5-0-2018-05-02" class="anchor"></a>Version 1.5.0 (2018-05-02)</h2>
<ul>
<li>Bioconductor 3.7 devel</li>
</ul>
</div>
- <div id="version-1-4-3-2018-08-20" class="section level2">
+<div id="version-1-4-3-2018-08-20" class="section level2">
<h2 class="hasAnchor">
<a href="#version-1-4-3-2018-08-20" class="anchor"></a>Version 1.4.3 (2018-08-20)</h2>
<ul>
<li>Fix bug in BASiCSEstimate when no spike-ins provided</li>
</ul>
</div>
- <div id="version-1-4-2-2018-08-16" class="section level2">
+<div id="version-1-4-2-2018-08-16" class="section level2">
<h2 class="hasAnchor">
<a href="#version-1-4-2-2018-08-16" class="anchor"></a>Version 1.4.2 (2018-08-16)</h2>
<ul>
@@ -193,7 +197,7 @@
<li>Add new BASiCS tests</li>
</ul>
</div>
- <div id="version-1-4-1-2018-06-12" class="section level2">
+<div id="version-1-4-1-2018-06-12" class="section level2">
<h2 class="hasAnchor">
<a href="#version-1-4-1-2018-06-12" class="anchor"></a>Version 1.4.1 (2018-06-12)</h2>
<ul>
@@ -201,6 +205,7 @@
<li>Correct p-value cutoff in normality test</li>
<li>Sample library sizes for normality testing if > 5000 cells</li>
</ul>
+</div>
</div>
<div id="version-1-4-0-2018-05-02" class="section level1">
<h1 class="page-header">
@@ -664,16 +669,7 @@
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
- <li><a href="#version-1-5-8-2018-10-22">1.5.8</a></li>
- <li><a href="#version-1-5-7-2018-10-03">1.5.7</a></li>
- <li><a href="#version-1-5-4-2018-08-30">1.5.4</a></li>
- <li><a href="#version-1-5-3-2018-08-20">1.5.3</a></li>
- <li><a href="#version-1-5-2-2018-08-16">1.5.2</a></li>
- <li><a href="#version-1-5-1-2018-06-12">1.5.1</a></li>
- <li><a href="#version-1-5-0-2018-05-02">1.5.0</a></li>
- <li><a href="#version-1-4-3-2018-08-20">1.4.3</a></li>
- <li><a href="#version-1-4-2-2018-08-16">1.4.2</a></li>
- <li><a href="#version-1-4-1-2018-06-12">1.4.1</a></li>
+ <li><a href="#version-1-6-0-2018-11-01">1.6.0</a></li>
<li><a href="#version-1-4-0-2018-05-02">1.4.0</a></li>
<li><a href="#version-1-2-0-2017-10-30">1.2.0</a></li>
<li><a href="#version-1-0-0-2017-04-28">1.0.0</a></li>
diff --git a/docs/reference/BASiCSEstimate.html b/docs/reference/BASiCSEstimate.html
index f8151d0cfe0e333269a80bb68bec5a4415e574b3..b77949c9b0c34f718d0ddc46c5c1b5877dad3305 100644
--- a/docs/reference/BASiCSEstimate.html
+++ b/docs/reference/BASiCSEstimate.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/BASiCSParams.html b/docs/reference/BASiCSParams.html
index 7ed012a0a6a69365d784b5d480651955c411c173..485483fdf345a0dadc0ee3c7401e13c25f4fdb24 100644
--- a/docs/reference/BASiCSParams.html
+++ b/docs/reference/BASiCSParams.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/BASiCSSimulate.html b/docs/reference/BASiCSSimulate.html
index 3a6b5ebd9749b4c37a4822c0650dfeaff3cfb8d0..64893c46a4a263dfcb44a55244bc8be4c1caf246 100644
--- a/docs/reference/BASiCSSimulate.html
+++ b/docs/reference/BASiCSSimulate.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/Lun2Params.html b/docs/reference/Lun2Params.html
index 546979f037aa507b0a96fb33f54f9901eafc5709..c1b75330d3607ca04c91d2fad7bd47e3b5390305 100644
--- a/docs/reference/Lun2Params.html
+++ b/docs/reference/Lun2Params.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/LunParams.html b/docs/reference/LunParams.html
index 6362e4623108f8db7f109b8c6fe83eab90326b68..05d3be77e873eed925341996eb889255f37e3b5c 100644
--- a/docs/reference/LunParams.html
+++ b/docs/reference/LunParams.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/MFAParams.html b/docs/reference/MFAParams.html
index 6a6ff08d27b91aa6341bfef48668efaed23b3099..312899b4db0fd1588922f1f5ec70c5bc31dc4aec 100644
--- a/docs/reference/MFAParams.html
+++ b/docs/reference/MFAParams.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/Params.html b/docs/reference/Params.html
index 7ead7db29f3c74e55627a97917a5920016b830ee..823135c4317f248ba6bdd26ed12691db0c481165 100644
--- a/docs/reference/Params.html
+++ b/docs/reference/Params.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/PhenoParams.html b/docs/reference/PhenoParams.html
index ad35b95bd26bedc23e3b91c5e51a813285577246..488e7bc623eb72fb3824ac198af1ebe43726ebd6 100644
--- a/docs/reference/PhenoParams.html
+++ b/docs/reference/PhenoParams.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/SCDDParams.html b/docs/reference/SCDDParams.html
index 3ff52225c4ba8dc1dab7c9e4f3a21cc04d0611b6..fedaa60f564ac5444e8e9240f5411bd0a252ec2d 100644
--- a/docs/reference/SCDDParams.html
+++ b/docs/reference/SCDDParams.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/SimpleParams.html b/docs/reference/SimpleParams.html
index 978c0d888f9c5d61ec929c35f6fc459bd105d6ab..c2a873517ff7c1f6dac33f0a6614706a74b48f46 100644
--- a/docs/reference/SimpleParams.html
+++ b/docs/reference/SimpleParams.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/SparseDCParams.html b/docs/reference/SparseDCParams.html
index 6c180f7cb6ef69cd3b519e61be42659d19e71f12..b7d4db37d8cd1da576b3d675fbd84bebf868448a 100644
--- a/docs/reference/SparseDCParams.html
+++ b/docs/reference/SparseDCParams.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/SplatParams.html b/docs/reference/SplatParams.html
index 8869ec7953ba898accf1491ad5b2deeaffdcb10c..4c561669eb0a430379ca01190e0d97fb4e1d578c 100644
--- a/docs/reference/SplatParams.html
+++ b/docs/reference/SplatParams.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/ZINBParams.html b/docs/reference/ZINBParams.html
index 28a381f36efb22b8cb256f6c16d12a330b46a53d..169cbe1323c90c01350e4d78f3e99d6e1bcca9ec 100644
--- a/docs/reference/ZINBParams.html
+++ b/docs/reference/ZINBParams.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/addFeatureStats.html b/docs/reference/addFeatureStats.html
index e7c69138a9b8b7ed48d3da962083566735ad63a0..3d0f6587514179774a2e720f4907e369c8964208 100644
--- a/docs/reference/addFeatureStats.html
+++ b/docs/reference/addFeatureStats.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/addGeneLengths.html b/docs/reference/addGeneLengths.html
index de181056d99aa0201e411f34c20a5626315c0a8c..b0b429d17e9745500482f3f0654d5f36bcd475b6 100644
--- a/docs/reference/addGeneLengths.html
+++ b/docs/reference/addGeneLengths.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
@@ -175,14 +175,14 @@ vector.</p>
<pre class="examples"><div class='input'><span class='co'># Default generate method</span>
<span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>()</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'>addGeneLengths</span>(<span class='no'>sce</span>)
<span class='fu'>head</span>(<span class='fu'>rowData</span>(<span class='no'>sce</span>))</div><div class='output co'>#> DataFrame with 6 rows and 3 columns
-#> Gene GeneMean Length
-#> <factor> <numeric> <numeric>
-#> Gene1 Gene1 12.827219643517 916
-#> Gene2 Gene2 1.92490265787296 4897
-#> Gene3 Gene3 0.048568954144492 2808
-#> Gene4 Gene4 0.991640968123529 2910
-#> Gene5 Gene5 0.798837709521328 2011
-#> Gene6 Gene6 0.507440151502259 8228</div><div class='input'># Sample method (human coding genes)
+#> Gene GeneMean Length
+#> <factor> <numeric> <numeric>
+#> 1 Gene1 6.69884498929011 1918
+#> 2 Gene2 13.0546862619417 3442
+#> 3 Gene3 0.0179089352105092 1515
+#> 4 Gene4 2.04424418437723 980
+#> 5 Gene5 0.293059507696467 2298
+#> 6 Gene6 0.371133536944445 1041</div><div class='input'># Sample method (human coding genes)
</div><span class='co'># NOT RUN {</span>
<span class='fu'>library</span>(<span class='no'>TxDb.Hsapiens.UCSC.hg19.knownGene</span>)
<span class='fu'>library</span>(<span class='no'>GenomicFeatures</span>)
diff --git a/docs/reference/bridge.html b/docs/reference/bridge.html
index e5376cb204cd6481faf5c4536101c2203445a062..4998f490935e58b5fa089f9c380f71b9528e5712 100644
--- a/docs/reference/bridge.html
+++ b/docs/reference/bridge.html
@@ -74,7 +74,7 @@ a random walk with fixed end points." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/compareSCEs.html b/docs/reference/compareSCEs.html
index 37a28f62215f32b0e7c83b68cb807b9a2c806979..7c6ec686ec0bf21b635d429b62a0cf574e4c7f5f 100644
--- a/docs/reference/compareSCEs.html
+++ b/docs/reference/compareSCEs.html
@@ -74,7 +74,7 @@ basic plots comparing them." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
@@ -186,15 +186,16 @@ compare.</p></td>
</dl></p></dd>
</dl>
<p>The plots returned by this function are created using
-<code><a href='http://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></code> and are only a sample of the kind of plots you
+<code><a href='ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code> and are only a sample of the kind of plots you
might like to consider. The data used to create these plots is also returned
and should be in the correct format to allow you to create further plots
-using <code><a href='http://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></code>.</p>
+using <code><a href='ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>comparison</span> <span class='kw'><-</span> <span class='fu'>compareSCEs</span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>))
-<span class='fu'>names</span>(<span class='no'>comparison</span>)</div><div class='output co'>#> [1] "FeatureData" "PhenoData" "Plots" </div><div class='input'><span class='fu'>names</span>(<span class='no'>comparison</span>$<span class='no'>Plots</span>)</div><div class='output co'>#> [1] "Means" "Variances" "MeanVar" "LibrarySizes" "ZerosGene"
+ <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>comparison</span> <span class='kw'><-</span> <span class='fu'>compareSCEs</span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>))</div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
+#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
+#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='input'><span class='fu'>names</span>(<span class='no'>comparison</span>)</div><div class='output co'>#> [1] "FeatureData" "PhenoData" "Plots" </div><div class='input'><span class='fu'>names</span>(<span class='no'>comparison</span>$<span class='no'>Plots</span>)</div><div class='output co'>#> [1] "Means" "Variances" "MeanVar" "LibrarySizes" "ZerosGene"
#> [6] "ZerosCell" "MeanZeros" </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
diff --git a/docs/reference/diffSCEs.html b/docs/reference/diffSCEs.html
index 43cad8d36046bf0b0433141a69b9b8328d5b0220..4d07b6224d5c8f628cdb3f395e91064e01283508 100644
--- a/docs/reference/diffSCEs.html
+++ b/docs/reference/diffSCEs.html
@@ -74,7 +74,7 @@ basic plots comparing them to a reference." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
@@ -208,15 +208,16 @@ Q-Q plots are also returned.</p>
</dl></p></dd>
</dl>
<p>The plots returned by this function are created using
-<code><a href='http://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></code> and are only a sample of the kind of plots you
+<code><a href='ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code> and are only a sample of the kind of plots you
might like to consider. The data used to create these plots is also returned
and should be in the correct format to allow you to create further plots
-using <code><a href='http://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></code>.</p>
+using <code><a href='ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'>diffSCEs</span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)
-<span class='fu'>names</span>(<span class='no'>difference</span>)</div><div class='output co'>#> [1] "Reference" "FeatureData" "PhenoData" "Plots" "QQPlots" </div><div class='input'><span class='fu'>names</span>(<span class='no'>difference</span>$<span class='no'>Plots</span>)</div><div class='output co'>#> [1] "Means" "Variances" "MeanVar" "LibrarySizes" "ZerosGene"
+ <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'>diffSCEs</span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)</div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
+#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
+#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='input'><span class='fu'>names</span>(<span class='no'>difference</span>)</div><div class='output co'>#> [1] "Reference" "FeatureData" "PhenoData" "Plots" "QQPlots" </div><div class='input'><span class='fu'>names</span>(<span class='no'>difference</span>$<span class='no'>Plots</span>)</div><div class='output co'>#> [1] "Means" "Variances" "MeanVar" "LibrarySizes" "ZerosGene"
#> [6] "ZerosCell" "MeanZeros" </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
diff --git a/docs/reference/expandParams.html b/docs/reference/expandParams.html
index 15b3d167ec579ac0cbd3e4ab97612ed151116570..9641f4f9094e79da31119001477e204028a5a2d3 100644
--- a/docs/reference/expandParams.html
+++ b/docs/reference/expandParams.html
@@ -74,7 +74,7 @@ the number of groups." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/getLNormFactors.html b/docs/reference/getLNormFactors.html
index 9c5f85d428064c03e8a82710c9e3383a3a0969ef..b8be9d3872c4efd199d70598a8100ac4d82ec877 100644
--- a/docs/reference/getLNormFactors.html
+++ b/docs/reference/getLNormFactors.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/getParam.html b/docs/reference/getParam.html
index 5de9f6e6c5d74fc558ee9ce3642aeb43c828e420..8c155ecf4327e08d72c5b2daab516992e60079d8 100644
--- a/docs/reference/getParam.html
+++ b/docs/reference/getParam.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/getParams.html b/docs/reference/getParams.html
index ed428d6bcdd9a386cf016356d7fb87750ad38e2a..092e0b20bd42d1a8c5f01e85e6f79b8f514d5581 100644
--- a/docs/reference/getParams.html
+++ b/docs/reference/getParams.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/getPathOrder.html b/docs/reference/getPathOrder.html
index 40df26e48f5c8231891e0f7cfdeb3b8c4e73ef9a..635238f59a2f5f86e84416e71f87e7355cb0c37f 100644
--- a/docs/reference/getPathOrder.html
+++ b/docs/reference/getPathOrder.html
@@ -74,7 +74,7 @@ already been simulated." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 2524f412b75129f2da98f353572d0bc3bcb0e89c..1c2b8fa9ee7df642e1a4c20eb8851720744fe83b 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -70,7 +70,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/listSims.html b/docs/reference/listSims.html
index 0a5b1c51b50196bd57d34e19b0858038ec35f867..d158ea8253b6f503ec203d3f76cfa02769547641 100644
--- a/docs/reference/listSims.html
+++ b/docs/reference/listSims.html
@@ -74,7 +74,7 @@ brief description." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/logistic.html b/docs/reference/logistic.html
index 38f322b6ffa958c6d07f6e51d750715078fe9bf0..44e8eb62700f43206fe14e46baacfdffe0a79509 100644
--- a/docs/reference/logistic.html
+++ b/docs/reference/logistic.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/lun2Estimate.html b/docs/reference/lun2Estimate.html
index 9c7dcab824404a114d8a3eb743e73e6a2399f7ed..9920f8fd4453ac2122b7ba4b8406f50d333c9e34 100644
--- a/docs/reference/lun2Estimate.html
+++ b/docs/reference/lun2Estimate.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/lun2Simulate.html b/docs/reference/lun2Simulate.html
index 2402dc9a6e6d37bb335b5f79c9b088275ab73b1c..b2bca23ae47c2e28c39cdff29703de8fbe1285a4 100644
--- a/docs/reference/lun2Simulate.html
+++ b/docs/reference/lun2Simulate.html
@@ -75,7 +75,7 @@ analyses of single-cell RNA-seq data"." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/lunEstimate.html b/docs/reference/lunEstimate.html
index 489f315b703401b60180d437bbe9637dcc9b5016..ddcd718f385f3f7fb763c64a3ff7a2014713bcd2 100644
--- a/docs/reference/lunEstimate.html
+++ b/docs/reference/lunEstimate.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
@@ -175,7 +175,7 @@ for more details on the parameters.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 735696
+#> 2000 40 339641
#>
#> 9 additional parameters
#>
diff --git a/docs/reference/lunSimulate.html b/docs/reference/lunSimulate.html
index 4eb7e16b6becc0e4aabc82978f39555739ae7ee0..d43eebb8486af6135d759a6a496e704f75987950 100644
--- a/docs/reference/lunSimulate.html
+++ b/docs/reference/lunSimulate.html
@@ -75,7 +75,7 @@ sequencing data with many zero counts"." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/makeCompPanel.html b/docs/reference/makeCompPanel.html
index 1311440208cf3962b1497426933536aa399191fe..03f969b7e7aa0b950ca1741b8d6beaf5bf9aaeca 100644
--- a/docs/reference/makeCompPanel.html
+++ b/docs/reference/makeCompPanel.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/makeDiffPanel.html b/docs/reference/makeDiffPanel.html
index d8875d34d096eb36b306f781a70d6a422572aa49..d6436a9dfb27d45fa9ac0700640bb98d4e77f629 100644
--- a/docs/reference/makeDiffPanel.html
+++ b/docs/reference/makeDiffPanel.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/makeOverallPanel.html b/docs/reference/makeOverallPanel.html
index cab70531950530de6bd95eb9aad50bbaa1b3a561..793908e3c1a371f73b74d73a691b12f371d423d4 100644
--- a/docs/reference/makeOverallPanel.html
+++ b/docs/reference/makeOverallPanel.html
@@ -74,7 +74,7 @@ single panel." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/mfaEstimate.html b/docs/reference/mfaEstimate.html
index 3793dae134421177a3e7dba6de1dc7e43daedc01..94fb5551ad035f0a3f7c3517b04e2c7bbe5b71db 100644
--- a/docs/reference/mfaEstimate.html
+++ b/docs/reference/mfaEstimate.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
@@ -172,7 +172,7 @@ details on the parameters.</p>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 735696
+#> 2000 40 339641
#>
#> 4 additional parameters
#>
diff --git a/docs/reference/mfaSimulate.html b/docs/reference/mfaSimulate.html
index 0c7303afb9ec8b52c035e3c80a2a20d2f669815d..814e1902a4b940fe0ae18be7411487e4dfc273ef 100644
--- a/docs/reference/mfaSimulate.html
+++ b/docs/reference/mfaSimulate.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/newParams.html b/docs/reference/newParams.html
index 9d2b43a63f1618096a727f5d94ca1e7ed0450fe1..cb5a377ef104c95089f47c47e7c0d923fb979f72 100644
--- a/docs/reference/newParams.html
+++ b/docs/reference/newParams.html
@@ -74,7 +74,7 @@ Params subtypes." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/phenoEstimate.html b/docs/reference/phenoEstimate.html
index 6c880d3f97a080afcf5fc4a4f6c52463d4343946..1d64ab654d0b7cb3ec87d728644ca939a399b88a 100644
--- a/docs/reference/phenoEstimate.html
+++ b/docs/reference/phenoEstimate.html
@@ -74,7 +74,7 @@ dataset." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
@@ -173,7 +173,7 @@ See <code><a href='PhenoParams.html'>PhenoParams</a></code> for more details on
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 735696
+#> 2000 40 339641
#>
#> 4 additional parameters
#>
diff --git a/docs/reference/phenoSimulate.html b/docs/reference/phenoSimulate.html
index e31ab446077c45af4c115d9a688d641ad55ad783..3291797d543c763a37465293d7e4c855f017952c 100644
--- a/docs/reference/phenoSimulate.html
+++ b/docs/reference/phenoSimulate.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/rbindMatched.html b/docs/reference/rbindMatched.html
index 6e954168551952efcf0fded0e0ea0b87f2d062ff..095fc5c5af09767657bbc15bc064442db907ed5c 100644
--- a/docs/reference/rbindMatched.html
+++ b/docs/reference/rbindMatched.html
@@ -74,7 +74,7 @@ to both." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/scDDEstimate.html b/docs/reference/scDDEstimate.html
index 93929781b209bbe875bf8cf3066de41522992e0a..5a3cac4e0d852b6a115142d8a3ef1ee49dd7e058 100644
--- a/docs/reference/scDDEstimate.html
+++ b/docs/reference/scDDEstimate.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/scDDSimulate.html b/docs/reference/scDDSimulate.html
index b01de890d63bdcf4d445698643312717cafbe7a5..36e73d6b14d1ce8f2b11ab3a23f1561167a949b3 100644
--- a/docs/reference/scDDSimulate.html
+++ b/docs/reference/scDDSimulate.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/setParam.html b/docs/reference/setParam.html
index 49411deb8b6ca1de24d9e14d6b16157afaadefcd..91bbe440db4b12811d75fb17276db54c201e7d79 100644
--- a/docs/reference/setParam.html
+++ b/docs/reference/setParam.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
@@ -181,7 +181,7 @@
#>
#> Global:
#> (GENES) (Cells) [Seed]
-#> 100 100 735696
+#> 100 100 339641
#>
#> 3 additional parameters
#>
diff --git a/docs/reference/setParamUnchecked.html b/docs/reference/setParamUnchecked.html
index bde2033d2e2ed2ad20e0feb959f1c4cc39a3822b..bfcd4f0dddfd3fe964f476452cce461f258f4bd5 100644
--- a/docs/reference/setParamUnchecked.html
+++ b/docs/reference/setParamUnchecked.html
@@ -74,7 +74,7 @@ VALIDITY!" />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/setParams.html b/docs/reference/setParams.html
index ff6bfa813aa7e22874061b9bcd8a6ef979611fde..370d259627b5e21a7ac26ec6c848ba811b8e8e67 100644
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<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
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@@ -167,7 +167,7 @@ them manually), see examples.</p>
#>
#> Global:
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@@ -185,7 +185,7 @@ them manually), see examples.</p>
#>
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@@ -203,7 +203,7 @@ them manually), see examples.</p>
#>
#> Global:
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<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
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diff --git a/docs/reference/showDFs.html b/docs/reference/showDFs.html
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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diff --git a/docs/reference/showPP.html b/docs/reference/showPP.html
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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diff --git a/docs/reference/showValues.html b/docs/reference/showValues.html
index 8d27fffcd29417b80dd8076342fd08f63c0bf516..4cfdd073914d7fff488d986150676a65b1371db6 100644
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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diff --git a/docs/reference/simpleEstimate.html b/docs/reference/simpleEstimate.html
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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@@ -173,7 +173,7 @@ details on the parameters.</p>
#>
#> Global:
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diff --git a/docs/reference/simpleSimulate.html b/docs/reference/simpleSimulate.html
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--- a/docs/reference/simpleSimulate.html
+++ b/docs/reference/simpleSimulate.html
@@ -74,7 +74,7 @@ simulated library sizes, differential expression etc." />
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/sparseDCEstimate.html b/docs/reference/sparseDCEstimate.html
index b2c833be3b9cad461ee266a65f836095c05295fe..d9a9ce6125753b0949bc443351ca6d1aa779d4da 100644
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
@@ -196,7 +196,7 @@ input data. The counts are preprocessed using
#>
#> Global:
#> (GENES) (CELLS) [Seed]
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diff --git a/docs/reference/sparseDCSimulate.html b/docs/reference/sparseDCSimulate.html
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<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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diff --git a/docs/reference/splatEstBCV.html b/docs/reference/splatEstBCV.html
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/splatEstDropout.html b/docs/reference/splatEstDropout.html
index 2e0ad6a4b47a8f15d9f7c0746c394b67114ac216..4318a7b57c41c65428b54be38299f604a9770767 100644
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/splatEstLib.html b/docs/reference/splatEstLib.html
index e9cc98221263acf8f8c4f2ece36008b98daa50b8..93c9cb07c9f4d7389ebbb90e221f62e6eac299fd 100644
--- a/docs/reference/splatEstLib.html
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/splatEstMean.html b/docs/reference/splatEstMean.html
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
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diff --git a/docs/reference/splatEstOutlier.html b/docs/reference/splatEstOutlier.html
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/splatEstimate.html b/docs/reference/splatEstimate.html
index d7ecc12442d10979fe425476a6cbbc889c9ed350..0f4552f637b38aba8b2ad19cbdf4be83a18ebfe4 100644
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
@@ -175,7 +175,7 @@ containing count data to estimate parameters from.</p></td>
#>
#> Global:
#> (GENES) (CELLS) [Seed]
-#> 2000 40 735696
+#> 2000 40 339641
#>
#> 28 additional parameters
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diff --git a/docs/reference/splatSimBCVMeans.html b/docs/reference/splatSimBCVMeans.html
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+++ b/docs/reference/splatSimBCVMeans.html
@@ -75,7 +75,7 @@ and inverse gamma distribution." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
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diff --git a/docs/reference/splatSimBatchCellMeans.html b/docs/reference/splatSimBatchCellMeans.html
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@@ -74,7 +74,7 @@ factors." />
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/splatSimBatchEffects.html b/docs/reference/splatSimBatchEffects.html
index 9619bb64ffeff671cf9beaaacab2e9c9a063fba8..c1ac60ccae078ef74f1247e89b6215b57fd7476a 100644
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/splatSimCellMeans.html b/docs/reference/splatSimCellMeans.html
index 0ba29af6197248c2a193d3dbb4fabfe3c875cb28..40284a6588a5a741004bced193284c91cb5d4563 100644
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@@ -77,7 +77,7 @@ means are adjusted for each cell's expected library size." />
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/splatSimDE.html b/docs/reference/splatSimDE.html
index e926017ea744f72ddb4063f82f4d3b38c4442b54..29218a3f7c2c4b8a515e6e7a0928eee2434c3827 100644
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@@ -76,7 +76,7 @@ they are simulated in the correct order." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/splatSimDropout.html b/docs/reference/splatSimDropout.html
index e1c16017a7c91b417175b5a89aa1cec0ba153535..8958426b91f441ced246fac98b5f5619bf6a702a 100644
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/splatSimGeneMeans.html b/docs/reference/splatSimGeneMeans.html
index a1fb1e3fef5d25b7f82f8ed91dbd43dcc4c7a4e8..db293c3f54d3493935efc35c0f1075a2f7ef1b00 100644
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/splatSimLibSizes.html b/docs/reference/splatSimLibSizes.html
index 52f93e46b05a8bd3501f13c84bfaaa7a9aa3f997..4135c53049405dda6dc13f56d65820bc3605daef 100644
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@@ -75,7 +75,7 @@ negative values are set to half the minimum non-zero value." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/splatSimTrueCounts.html b/docs/reference/splatSimTrueCounts.html
index d533065e10713680aa5309c1299cfe4487a86621..469200582f65b79a1ce8e91c20ceeb8d6e7ab06c 100644
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@@ -75,7 +75,7 @@ group (or path position), expected library size and BCV." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/splatSimulate.html b/docs/reference/splatSimulate.html
index 3ffad504f056829681e7e855bba924fda72f3c6f..07bd60fddf73ee4bf94e96ee5cdf249d88a135cb 100644
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@@ -74,7 +74,7 @@ the Splat method." />
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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diff --git a/docs/reference/splatter.html b/docs/reference/splatter.html
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--- a/docs/reference/splatter.html
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@@ -74,7 +74,7 @@ simulation of single-cell RNA-seq count data." />
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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diff --git a/docs/reference/summariseDiff.html b/docs/reference/summariseDiff.html
index 6b76f3d6690a822158bd2dbf9b9382b1d94f0481..e7c564d57662c546424b4dc188f09f156192b130 100644
--- a/docs/reference/summariseDiff.html
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@@ -75,7 +75,7 @@ Error (RMSE) for the various properties and ranks them." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
@@ -147,22 +147,23 @@ Error (RMSE) for the various properties and ranks them.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'><a href='diffSCEs.html'>diffSCEs</a></span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)
-<span class='no'>summary</span> <span class='kw'><-</span> <span class='fu'>summariseDiff</span>(<span class='no'>difference</span>)
-<span class='fu'>head</span>(<span class='no'>summary</span>)</div><div class='output co'>#> Dataset Statistic MAD MADScaled MADRank MAE MAEScaled
-#> 1 Splat Mean 2.543821 NaN 1 2.490035 NaN
-#> 2 Splat Variance 10.495774 NaN 1 9.766863 NaN
-#> 3 Splat ZerosGene 35.000000 NaN 1 41.330000 NaN
-#> 4 Splat MeanVar 8.419913 NaN 1 11.469025 NaN
-#> 5 Splat MeanZeros 40.000000 NaN 1 41.830000 NaN
-#> 6 Splat LibSize 57521.500000 NaN 1 59002.500000 NaN
+ <pre class="examples"><div class='input'><span class='no'>sim1</span> <span class='kw'><-</span> <span class='fu'><a href='splatSimulate.html'>splatSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>batchCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Getting parameters...</span></div><div class='output co'>#> <span class='message'>Creating simulation object...</span></div><div class='output co'>#> <span class='message'>Simulating library sizes...</span></div><div class='output co'>#> <span class='message'>Simulating gene means...</span></div><div class='output co'>#> <span class='message'>Simulating BCV...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Simulating dropout (if needed)...</span></div><div class='output co'>#> <span class='message'>Done!</span></div><div class='input'><span class='no'>sim2</span> <span class='kw'><-</span> <span class='fu'><a href='simpleSimulate.html'>simpleSimulate</a></span>(<span class='kw'>nGenes</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>nCells</span> <span class='kw'>=</span> <span class='fl'>20</span>)</div><div class='output co'>#> <span class='message'>Simulating means...</span></div><div class='output co'>#> <span class='message'>Simulating counts...</span></div><div class='output co'>#> <span class='message'>Creating final dataset...</span></div><div class='input'><span class='no'>difference</span> <span class='kw'><-</span> <span class='fu'><a href='diffSCEs.html'>diffSCEs</a></span>(<span class='fu'>list</span>(<span class='kw'>Splat</span> <span class='kw'>=</span> <span class='no'>sim1</span>, <span class='kw'>Simple</span> <span class='kw'>=</span> <span class='no'>sim2</span>), <span class='kw'>ref</span> <span class='kw'>=</span> <span class='st'>"Simple"</span>)</div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
+#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='output co'>#> <span class='message'>Note that the names of some metrics have changed, see 'Renamed metrics' in ?calculateQCMetrics.</span>
+#> <span class='message'>Old names are currently maintained for back-compatibility, but may be removed in future releases.</span></div><div class='input'><span class='no'>summary</span> <span class='kw'><-</span> <span class='fu'>summariseDiff</span>(<span class='no'>difference</span>)
+<span class='fu'>head</span>(<span class='no'>summary</span>)</div><div class='output co'>#> Dataset Statistic MAD MADScaled MADRank MAE MAEScaled
+#> 1 Splat Mean 2.91420 NaN 1 2.699822 NaN
+#> 2 Splat Variance 11.87313 NaN 1 10.433146 NaN
+#> 3 Splat ZerosGene 40.00000 NaN 1 45.545000 NaN
+#> 4 Splat MeanVar 11.35143 NaN 1 12.185829 NaN
+#> 5 Splat MeanZeros 45.00000 NaN 1 45.065000 NaN
+#> 6 Splat LibSize 59524.50000 NaN 1 62164.900000 NaN
#> MAERank RMSE RMSEScaled RMSERank
-#> 1 1 3.004655 NaN 1
-#> 2 1 12.483217 NaN 1
-#> 3 1 45.764615 NaN 1
-#> 4 1 14.691833 NaN 1
-#> 5 1 51.732968 NaN 1
-#> 6 1 60005.941034 NaN 1</div></pre>
+#> 1 1 3.240761 NaN 1
+#> 2 1 13.125369 NaN 1
+#> 3 1 49.070103 NaN 1
+#> 4 1 15.258433 NaN 1
+#> 5 1 54.676549 NaN 1
+#> 6 1 63270.772188 NaN 1</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/winsorize.html b/docs/reference/winsorize.html
index 8decdf3fca20466bd255b481d2c09938f3b4236d..423b317f581470f25452136c1a20df0a65903927 100644
--- a/docs/reference/winsorize.html
+++ b/docs/reference/winsorize.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/zinbEstimate.html b/docs/reference/zinbEstimate.html
index 85ccb9fb1df240cbe183527159ff53d9b5ccf645..ebe5311b8284dd77fa64a52bf217cd8bf49c1467 100644
--- a/docs/reference/zinbEstimate.html
+++ b/docs/reference/zinbEstimate.html
@@ -74,7 +74,7 @@ dataset." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>
diff --git a/docs/reference/zinbSimulate.html b/docs/reference/zinbSimulate.html
index 2e4005123180dda73d28f7f21b3a6eddf6fbf6d3..760c43149e4ee03a61087feb9656cf4da6cbe1b2 100644
--- a/docs/reference/zinbSimulate.html
+++ b/docs/reference/zinbSimulate.html
@@ -73,7 +73,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">Splatter</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.5.8</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
</span>
</div>