From 46741af554baae055978f228d5459c773cb5eed9 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Wed, 3 Jan 2018 16:35:51 +1100
Subject: [PATCH] Fix vignette error
---
DESCRIPTION | 4 ++--
NEWS.md | 8 ++++++++
R/compare.R | 4 ++--
vignettes/splatter.Rmd | 15 +++++++++++----
4 files changed, 23 insertions(+), 8 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 1a129b4..466ea86 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: splatter
Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 1.2.1
-Date: 2017-11-23
+Version: 1.3.1
+Date: 2018-01-03
Author: Luke Zappia
Authors@R:
c(person("Luke", "Zappia", role = c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index d80a6c6..dde2f7a 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,11 @@
+## Version 1.3.1 (2018-01-03)
+
+* Fix error in vignette caused by changes in scater
+
+## Version 1.3.0 (2018-01-03)
+
+* Bioconductor 3.7 devel
+
## Version 1.2.1 (2017-11-23)
* Fix zinbwave installation error
diff --git a/R/compare.R b/R/compare.R
index 6739fb9..fb1f270 100644
--- a/R/compare.R
+++ b/R/compare.R
@@ -75,7 +75,7 @@ compareSCEs <- function(sces, point.size = 0.1, point.alpha = 0.1,
rowData(sce)$Dataset <- name
colData(sce)$Dataset <- name
sce <- scater::calculateQCMetrics(sce)
- cpm(sce) <- scater::calculateCPM(sce, use.size.factors = FALSE)
+ cpm(sce) <- scater::calculateCPM(sce, use_size_factors = FALSE)
sce <- addFeatureStats(sce, "counts")
sce <- addFeatureStats(sce, "cpm")
sce <- addFeatureStats(sce, "cpm", log = TRUE)
@@ -301,7 +301,7 @@ diffSCEs <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
rowData(sce)$Dataset <- name
colData(sce)$Dataset <- name
sce <- scater::calculateQCMetrics(sce)
- cpm(sce) <- scater::calculateCPM(sce, use.size.factors = FALSE)
+ cpm(sce) <- scater::calculateCPM(sce, use_size_factors = FALSE)
sce <- addFeatureStats(sce, "counts")
sce <- addFeatureStats(sce, "cpm", log = TRUE)
colData(sce)$PctZero <- 100 * (1 - colData(sce)$total_features /
diff --git a/vignettes/splatter.Rmd b/vignettes/splatter.Rmd
index e72e866..ae895ee 100644
--- a/vignettes/splatter.Rmd
+++ b/vignettes/splatter.Rmd
@@ -278,7 +278,10 @@ get immediate access to other analysis packages, such as the plotting functions
in `scater`. For example we can make a PCA plot:
```{r pca}
-plotPCA(sim, exprs_values = "counts")
+# Use scater to calculate logcounts
+sim <- normalise(sim)
+# Plot PCA
+plotPCA(sim)
```
(**NOTE:** Your values and plots may look different as the simulation is random
@@ -336,7 +339,8 @@ printing progress messages.)
```{r groups}
sim.groups <- splatSimulate(group.prob = c(0.5, 0.5), method = "groups",
verbose = FALSE)
-plotPCA(sim.groups, colour_by = "Group", exprs_values = "counts")
+sim.groups <- normalise(sim.groups)
+plotPCA(sim.groups, colour_by = "Group")
```
As we have set both the group probabilites to 0.5 we should get approximately
@@ -354,7 +358,8 @@ method.
```{r paths}
sim.paths <- splatSimulate(method = "paths", verbose = FALSE)
-plotPCA(sim.paths, colour_by = "Step", exprs_values = "counts")
+sim.paths <- normalise(sim.paths)
+plotPCA(sim.paths, colour_by = "Step")
```
Here the colours represent the "step" of each cell or how far along the
@@ -373,7 +378,8 @@ cells are in each batch:
```{r batches}
sim.batches <- splatSimulate(batchCells = c(50, 50), verbose = FALSE)
-plotPCA(sim.batches, colour_by = "Batch", exprs_values = "counts")
+sim.batches <- normalise(sim.batches)
+plotPCA(sim.batches, colour_by = "Batch")
```
This looks at lot like when we simulated groups and that is because the process
@@ -386,6 +392,7 @@ that we aren't interested in (batch) and the wanted variation we are looking for
```{r batch-groups}
sim.groups <- splatSimulate(batchCells = c(50, 50), group.prob = c(0.5, 0.5),
method = "groups", verbose = FALSE)
+sim.groups <- normalise(sim.groups)
plotPCA(sim.groups, shape_by = "Batch", colour_by = "Group",
exprs_values = "counts")
```
--
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