Merge branch 'master' into basics

* master:
  Add extra.css
  Add index.md
  Add reference index
  Add _pkgdown.yml
  Add basic site
  Fix group factors bug

.Rbuildignore

@@ -4,4 +4,7 @@
 ^codecov\.yml$
 ^appveyor\.yml$
 ^NEWS\.md$
-^\.git*
\ No newline at end of file
+^\.git*
+^docs$
+^_pkgdown\.yml$
+^pkgdown$

DESCRIPTION

 Package: splatter
 Type: Package
 Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 1.1.3
-Date: 2017-07-20
+Version: 1.1.4
+Date: 2017-08-04
 Author: Luke Zappia
 Authors@R:
     c(person("Luke", "Zappia", role = c("aut", "cre"),

NEWS.md

-# 1.1.3
+## Version 1.1.4 (2017-08-04)
+
+* Fix group factors bug
+
+## Version 1.1.3 (2017-07-20)
 
 * Add verbose option to scDDEstimate
 * Change "mean-dropout" to "mean-zeros" in compareSCESets
 
-# 1.1.2
+## Version 1.1.2 (2017-07-16)
 
 * Update summariseDiff
 * Update scDDEstimate, now estimates gene types
 * Fix error in lun2Estimate
 * Import SummarizedExperiment to avoid warnings
 
-# 1.1.1
+## Version 1.1.1 (2017-07-07)
 
 * Add batch effects to Splat simulation
 * Make Splat group assignment probabilistic
 * Update SplatParams with new parameters
 
-# 1.1.0
+## Version 1.1.0 (2017-07-07)
 
 * Bioconductor 3.6 devel
 
-# 1.0.3
+## Version 1.0.3 (2017-05-26)
 
 * Update citation
 
-# 1.0.2
+## Version 1.0.2 (2017-05-15)
 
 * Fix error handling when fitting means
 
-# 1.0.1
+## Version 1.0.1 (2017-04-28)
 
 * Fix scales in some difference plots
 * Fix colours in difference plots
 * Fix panel legends
 
-# 1.0.0
+# Version 1.0.0 (2017-04-28)
 
 * Bioconductor 3.5 release
 
-# 0.99.15
+## Version 0.99.15 (2017-04-14)
 
 * Add summariseDiff function
 * Add BPPARAM argument to scDDSimulate
@@ -46,19 +50,19 @@
 * Add limits to zeros diff plots
 * Remove estimation of dropout.present
 
-# 0.99.14
+## Version 0.99.14 (2017-03-28)
 
 * Add functions for making comparison panels
 * Add panel section to vignette
 * Change variance plot scale (for consistency)
 
-# 0.99.13
+## Version 0.99.13 (2017-03-25)
 
 * Modify how Lun2Params stores gene paramters to use data.frame
 * Move sampling of genes/cells to lun2Simulate
 * Return to old Lun2 nGenes estimate
 
-# 0.99.12
+## Version 0.99.12 (2017-03-22)
 
 * Add diffSCESets function
 * Update compareSCESets plots
@@ -66,127 +70,127 @@
 * Modify how addFeatureStats names columns
 * Add infinte bcv.df warning to splatSimulate
 
-# 0.99.11
+## Version 0.99.11 (2017-03-20)
 
 * Add parallel option to lun2Estimate
 * Allow non-integer library sizes in Lun2Params
 * Adjust dropout eta value
 * Adjust comparison plots
 
-# 0.99.10
+## Version 0.99.10 (2017-03-07)
 
 * Improve Splat estimation procedure
 * Update default Splat parameters
 * Remove out.loProb Splat parameter
 * Add MeanZeros plot to compareSCESets
 
-# 0.99.9
+## Version 0.99.9 (2017-02-02)
 
 * Add addGeneLengths function
 * Update scDD reference
 
-# 0.99.8
+## Version 0.99.8 (2017-01-23)
 
 * Fix bug that meant non-linear path factors weren't stored in output
 
-# 0.99.7
+## Version 0.99.7 (2017-01-10)
 
 * Small changes to avoid NOTEs and reduce check time
 
-# 0.99.6
+## Version 0.99.6 (2016-12-29)
 
 * Add installation to vignette
 * Add detail about counts matrix to vignette
 * Replace 1:x with seq_len/seq_along
 
-# 0.99.5
+## Version 0.99.5 (2016-12-28)
 
 * Set R_TESTS environment
 
-# 0.99.4
+## Version 0.99.4 (2016-12-23)
 
 * Version bump to start build
 
-# splatter 0.99.3
+## Version 0.99.3 (2016-12-21)
 
 * Fix to match Bioconductor version of scDD
 * Add logo to repository
 
-# splatter 0.99.2
+## Version 0.99.2 (2016-12-13)
 
 * Add rownames, colnames to matrices in splatSimulate, lunSimulate
 * Bump R version to 3.4
 
-# splatter 0.99.1
+## Version 0.99.1 (2016-12-12)
 
 * Address Biocondutor build warnings, notes
 
-# splatter 0.99.0
+# Version 0.99.0 (2016-12-05)
 
 * Submit to Bioconductor
 
-# splatter 0.12.1
+## Version 0.12.1 (2016-11-25)
 
 * Fix bug in compareSCESets
 * Dataset order is now kept in plots
 
-# splatter 0.12.0
+## Version 0.12.0 (2016-10-25)
 
 * Add compareSCESets function
 * Update vignette
 * Fix LunParams validity bug
 * Add logo
 
-# splatter 0.11.1
+## Version 0.11.1 (2016-11-23)
 
 * Fix bug in splatSimulatePaths that caused NAs
 
-# splatter 0.11.0
+## Version 0.11.0 (2016-11-22)
 
 * Make compatible with Bioconductor 3.4
 
-# splatter 0.10.1
+## Version 0.10.1 (2016-10-17)
 
 * Fix error for SCESets in lun2Estimate, scDDEstimate
 
-# splatter 0.10.0
+## Version 0.10.0 (2016-10-16)
 
 * Add listSims function
 * Add vignette
 
-# splatter 0.9.0
+## Version 0.9.0 (2016-10-15)
 
 * Add scDD simulation
 
-# splatter 0.8.0
+## Version 0.8.0 (2016-10-15)
 
 * Add Lun2 simulation
 
-# splatter 0.7.0
+## Version 0.7.0 (2016-10-14)
 
 * Redesign how parameters are stored
 * Each simulation now has it's own S4 Params class
 * Modify exisiting simulations to use new parameter objects
 
-# splatter 0.6.0
+## Version 0.6.0 (2016-10-12)
 
 * Add Lun simulation
 * Modify splatParams to take Lun parameters
 
-# splatter 0.5.0
+## Version 0.5.0 (2016-10-12)
 
 * Add simple simulation
 
-# splatter 0.4.0
+## Version 0.4.0 (2016-10-12)
 
 * Add splatter simulations
 * Modify some parts of splatParams and fix bugs
 
-# splatter 0.3.0
+## Version 0.3.0 (2016-10-06)
 
 * Added parameter estimation functions
 
-# splatter 0.2.0
+## Version 0.2.0 (2016-10-06)
 
 * Added splatParams object
 * Added functions for interacting with splatParams

R/splat-simulate.R

@@ -501,7 +501,7 @@ splatSimGroupCellMeans <- function(sim, params) {
     cell.names <- pData(sim)$Cell
     gene.names <- fData(sim)$Gene
     groups <- pData(sim)$Group
-    group.names <- unique(groups)
+    group.names <- sort(unique(groups))
     exp.lib.sizes <- pData(sim)$ExpLibSize
     batch.means.cell <- get_exprs(sim, "BatchCellMeans")
 
@@ -535,7 +535,6 @@ splatSimPathCellMeans <- function(sim, params) {
     path.nonlinearProb <- getParam(params, "path.nonlinearProb")
     path.sigmaFac <- getParam(params, "path.sigmaFac")
     groups <- pData(sim)$Group
-    group.names <- unique(groups)
     exp.lib.sizes <- pData(sim)$ExpLibSize
     batch.means.cell <- get_exprs(sim, "BatchCellMeans")
 

_pkgdown.yml

+title: Splatter
+url: http://oshlack.github.io/splatter
+template:
+  params:
+    bootswatch: cosmo
+    ganalytics: UA-52309538-4
+reference:
+  - title: Parameters
+    desc: Parameters functions and classes
+    contents:
+      - '`getParam`'
+      - '`getParams`'
+      - '`Lun2Params`'
+      - '`LunParams`'
+      - '`newParams`'
+      - '`Params`'
+      - '`SCDDParams`'
+      - '`SimpleParams`'
+      - '`SplatParams`'
+      - '`setParam`'
+      - '`setParams`'
+  - title: Estimation
+    desc: Functions for estimating parameters
+    contents:
+      - '`lun2Estimate`'
+      - '`lunEstimate`'
+      - '`scDDEstimate`'
+      - '`simpleEstimate`'
+      - '`splatEstBCV`'
+      - '`splatEstDropout`'
+      - '`splatEstimate`'
+      - '`splatEstLib`'
+      - '`splatEstMean`'
+      - '`splatEstOutlier`'
+  - title: Simulation
+    desc: Functions for simulating datasets
+    contents:
+      - '`lun2Simulate`'
+      - '`lunSimulate`'
+      - '`scDDSimulate`'
+      - '`simpleSimulate`'
+      - '`splatSimBatchCellMeans`'
+      - '`splatSimBatchEffects`'
+      - '`splatSimBCVMeans`'
+      - '`splatSimCellMeans`'
+      - '`splatSimDE`'
+      - '`splatSimDropout`'
+      - '`splatSimGeneMeans`'
+      - '`splatSimLibSizes`'
+      - '`splatSimTrueCounts`'
+      - '`splatSimulate`'
+  - title: Comparison functions
+    desc: Functions for comparing datasets
+    contents:
+      - '`compareSCESets`'
+      - '`diffSCESets`'
+      - '`makeCompPanel`'
+      - '`makeDiffPanel`'
+      - '`makeOverallPanel`'
+      - '`summariseDiff`'
+  - title: Other exported functions
+    desc: Additional functions exported by Splatter
+    contents:
+      - '`addFeatureStats`'
+      - '`addGeneLengths`'
+      - '`listSims`'
+  - title: Internals
+    desc: Internal functions and helpers
+    contents:
+      - '`bridge`'
+      - '`expandParams`'
+      - '`getLNormFactors`'
+      - '`getPathOrder`'
+      - '`logistic`'
+      - '`rbindMatched`'
+      - '`setParamsUnchecked`'
+      - '`setParamUnchecked`'
+      - '`showPP`'
+      - '`winsorize`'

docs/articles/index.html

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+</div><!--/.navbar -->
+
+      
+      </header>
+
+      <div class="page-header">
+  <h1>Articles <small>version&nbsp;1.1.4</small></h1>
+</div>
+
+<div class="row">
+  <div class="col-md-9">
+    <div class="section ">
+      <h3>All vignettes</h3>
+      <p class="section-desc"></p>
+
+      <ul>
+        <li><a href="splatter.html">Introduction to Splatter</a></li>
+      </ul>
+    </div>
+  </div>
+</div>
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
+</div>
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+</li>
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+
+      
+      </header>
+
+      <div class="row">
+  <div class="contents col-md-9">
+
+    <div class="page-header">
+      <h1>Citation</h1>
+    </div>
+
+    <p>Zappia L, Phipson B and Oshlack A (2017).
+&ldquo;Splatter: Simulation Of Single-Cell RNA Sequencing Data.&rdquo;
+<em>bioRxiv</em>.
+doi: <a href="http://doi.org/10.1101/133173">10.1101/133173</a>, <a href="http://dx.doi.org/10.1101/133173">http://dx.doi.org/10.1101/133173</a>. 
+</p>
+    <pre>@Article{,
+  author = {Luke Zappia and Belinda Phipson and Alicia Oshlack},
+  title = {Splatter: Simulation Of Single-Cell RNA Sequencing Data},
+  journal = {bioRxiv},
+  year = {2017},
+  url = {http://dx.doi.org/10.1101/133173},
+  doi = {10.1101/133173},
+}</pre>
+    <div class="page-header">
+      <h1>Authors</h1>
+    </div>
+
+    <ul class="list-unstyled">
+      <li>
+        <p><strong>Luke Zappia</strong>. Author, maintainer.
+        </p>
+      </li>
+      <li>
+        <p><strong>Belinda Phipson</strong>. Author.
+        </p>
+      </li>
+      <li>
+        <p><strong>Alicia Oshlack</strong>. Author.
+        </p>
+      </li>
+    </ul>
+
+  </div>
+
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+
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+  <p>Developed by Luke Zappia, Belinda Phipson, Alicia Oshlack.</p>
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+
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+
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docs/extra.css

+.fl      {color: blue;}
+.fu      {color: #00ADEF;}  /* function */
+.ch,.st  {color: #F47920;}  /* string */
+.kw      {color: #7A52C7;}  /* keyword */
+.co      {color: #8DC63F;}  /* comment */
+
+.message { color: gray;   font-weight: bolder;}
+.error   { color: red;  font-weight: bolder;}
+.warning { color: purple; font-weight: bolder;}