Merge branch 'master' into devel

* master:
  Version 0.99.14
  Add panel function to vignette
  Change var plot scale
  Run checks
  Update panel functions
  Add makeOverallPanel function
  Add makeDiffPanel function
  Add options to comparison plots

From: Luke Zappia <lazappi@users.noreply.github.com>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@127789 bc3139a8-67e5-0310-9ffc-ced21a209358

DESCRIPTION

 Package: splatter
 Type: Package
 Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 0.99.13
-Date: 2017-03-25
+Version: 0.99.14
+Date: 2017-03-28
 Author: Luke Zappia
 Authors@R:
     c(person("Luke", "Zappia", role = c("aut", "cre"),
@@ -46,7 +46,8 @@ Suggests:
     BiocStyle,
     covr,
     S4Vectors,
-    SummarizedExperiment
+    SummarizedExperiment,
+    cowplot
 biocViews: SingleCell, RNASeq, Transcriptomics, GeneExpression, Sequencing,
     Software
 URL: https://github.com/Oshlack/splatter

NAMESPACE

@@ -20,6 +20,9 @@ export(lun2Estimate)
 export(lun2Simulate)
 export(lunEstimate)
 export(lunSimulate)
+export(makeCompPanel)
+export(makeDiffPanel)
+export(makeOverallPanel)
 export(newLun2Params)
 export(newLunParams)
 export(newSCDDParams)
@@ -58,17 +61,20 @@ importFrom(checkmate,checkIntegerish)
 importFrom(checkmate,checkNumber)
 importFrom(checkmate,checkNumeric)
 importFrom(ggplot2,aes_string)
+importFrom(ggplot2,element_blank)
 importFrom(ggplot2,geom_abline)
 importFrom(ggplot2,geom_boxplot)
 importFrom(ggplot2,geom_hline)
 importFrom(ggplot2,geom_point)
 importFrom(ggplot2,geom_smooth)
-importFrom(ggplot2,geom_violin)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,ggtitle)
+importFrom(ggplot2,scale_colour_manual)
+importFrom(ggplot2,scale_fill_manual)
 importFrom(ggplot2,scale_x_log10)
 importFrom(ggplot2,scale_y_continuous)
 importFrom(ggplot2,scale_y_log10)
+importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_minimal)
 importFrom(ggplot2,xlab)
 importFrom(ggplot2,ylab)

NEWS.md

+# 0.99.14
+
+* Add functions for making comparison panels
+* Add panel section to vignette
+* Change variance plot scale (for consistency)
+
 # 0.99.13
 
 * Modify how Lun2Params stores gene paramters to use data.frame

man/compareSCESets.Rd

@@ -4,10 +4,19 @@
 \alias{compareSCESets}
 \title{Compare SCESet objects}
 \usage{
-compareSCESets(sces)
+compareSCESets(sces, point.size = 0.1, point.alpha = 0.1, fits = TRUE,
+  colours = NULL)
 }
 \arguments{
 \item{sces}{named list of SCESet objects to combine and compare.}
+
+\item{point.size}{size of points in scatter plots.}
+
+\item{point.alpha}{opacity of points in scatter plots.}
+
+\item{fits}{whether to include fits in scatter plots.}
+
+\item{colours}{vector of colours to use for each dataset.}
 }
 \value{
 List containing the combined datasets and plots.

man/diffSCESets.Rd

@@ -4,12 +4,21 @@
 \alias{diffSCESets}
 \title{Diff SCESet objects}
 \usage{
-diffSCESets(sces, ref)
+diffSCESets(sces, ref, point.size = 0.1, point.alpha = 0.1, fits = TRUE,
+  colours = NULL)
 }
 \arguments{
 \item{sces}{named list of SCESet objects to combine and compare.}
 
 \item{ref}{string giving the name of the SCESet to use as the reference}
+
+\item{point.size}{size of points in scatter plots.}
+
+\item{point.alpha}{opacity of points in scatter plots.}
+
+\item{fits}{whether to include fits in scatter plots.}
+
+\item{colours}{vector of colours to use for each dataset.}
 }
 \value{
 List containing the combined datasets and plots.

man/makeCompPanel.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/compare.R
+\name{makeCompPanel}
+\alias{makeCompPanel}
+\title{Make comparison panel}
+\usage{
+makeCompPanel(comp, title = "Comparison", labels = c("Means", "Variance",
+  "Mean-variance relationship", "Library size", "Zeros per gene",
+  "Zeros per cell", "Mean-zeros relationship"))
+}
+\arguments{
+\item{comp}{list returned by \code{\link{compareSCESets}}.}
+
+\item{title}{title for the panel.}
+
+\item{labels}{vector of labels for each of the seven plots.}
+}
+\value{
+Combined panel plot
+}
+\description{
+Combine the plots from \code{compareSCESets} into a single panel.
+}
+\examples{
+\dontrun{
+sim1 <- splatSimulate(nGenes = 1000, groupCells = 20)
+sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
+comparison <- compareSCESets(list(Splat = sim1, Simple = sim2))
+panel <- makeCompPanel(comparison)
+}
+
+}

man/makeDiffPanel.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/compare.R
+\name{makeDiffPanel}
+\alias{makeDiffPanel}
+\title{Make difference panel}
+\usage{
+makeDiffPanel(diff, title = "Difference comparison", labels = c("Means",
+  "Variance", "Library size", "Zeros per cell", "Zeros per gene",
+  "Mean-variance relationship", "Mean-zeros relationship"))
+}
+\arguments{
+\item{diff}{list returned by \code{\link{diffSCESets}}.}
+
+\item{title}{title for the panel.}
+
+\item{labels}{vector of labels for each of the seven sections.}
+}
+\value{
+Combined panel plot
+}
+\description{
+Combine the plots from \code{diffSCESets} into a single panel.
+}
+\examples{
+\dontrun{
+sim1 <- splatSimulate(nGenes = 1000, groupCells = 20)
+sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
+difference <- diffSCESets(list(Splat = sim1, Simple = sim2), ref = "Simple")
+panel <- makeDiffPanel(difference)
+}
+
+}

man/makeOverallPanel.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/compare.R
+\name{makeOverallPanel}
+\alias{makeOverallPanel}
+\title{Make overall panel}
+\usage{
+makeOverallPanel(comp, diff, title = "Overall comparison",
+  row.labels = c("Means", "Variance", "Mean-variance relationship",
+  "Library size", "Zeros per cell", "Zeros per gene",
+  "Mean-zeros relationship"))
+}
+\arguments{
+\item{comp}{list returned by \code{\link{compareSCESets}}.}
+
+\item{diff}{list returned by \code{\link{diffSCESets}}.}
+
+\item{title}{title for the panel.}
+
+\item{row.labels}{vector of labels for each of the seven rows.}
+}
+\value{
+Combined panel plot
+}
+\description{
+Combine the plots from \code{compSCESets} and \code{diffSCESets} into a
+single panel.
+}
+\examples{
+\dontrun{
+sim1 <- splatSimulate(nGenes = 1000, groupCells = 20)
+sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
+comparison <- compSCESets(list(Splat = sim1, Simple = sim2))
+difference <- diffSCESets(list(Splat = sim1, Simple = sim2), ref = "Simple")
+panel <- makeOverallPanel(comparison, difference)
+}
+
+}

vignettes/splatter.Rmd

@@ -473,6 +473,30 @@ distributions.
 difference$QQPlots$Means
 ```
 
+## Making panels
+
+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 `makeCompPanel`, `makeDiffPanel` and `makeOverallPanel`.
+
+These functions combine the plots into a single panel using the `cowplot`
+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 `cowplot` provides a convenient function for saving the
+images. Here are some suggested parameters for outputting each of the panels:
+
+```{r save-panels, eval = FALSE}
+# This code is just an example and is not run
+panel <- makeCompPanel(comparison)
+cowplot::save_plot("comp_panel.png", panel, nrow = 4, ncol = 3)
+
+panel <- makeDiffPanel(difference)
+cowplot::save_plot("diff_panel.png", panel, nrow = 3, ncol = 5)
+
+panel <- makeOverallPanel(comparison, difference)
+cowplot::save_plot("overall_panel.png", panel, ncol = 4, nrow = 7)
+```
+
 # Session information {-}
 
 ```{r sessionInfo}