diff --git a/DESCRIPTION b/DESCRIPTION
index e4ed84ef585cb45400a7f4a6d4ccf7c964637570..c314d23b00e6b89a59b35115977100a678ecbe97 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
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
diff --git a/NAMESPACE b/NAMESPACE
index 2fac85b2ceab64fb95336e95c5c64a2a2688a917..e56ae21db7a3edff1c5cfb54b66055001bf93d77 100644
--- a/NAMESPACE
+++ b/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)
diff --git a/NEWS.md b/NEWS.md
index 124ce57ccd9cde8fe998b4341fb1d2feeb1fca9d..3936f24c405be1e5c880b3ce466d6f684cac493b 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,9 @@
+# 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
diff --git a/R/compare.R b/R/compare.R
index 23aa2710ccaf96391156870e6d71c745eb749580..4e0feb06054e2b8108172f6e47df11d2d872a3a4 100644
--- a/R/compare.R
+++ b/R/compare.R
@@ -4,6 +4,10 @@
#' comparing them.
#'
#' @param sces named list of SCESet objects to combine and compare.
+#' @param point.size size of points in scatter plots.
+#' @param point.alpha opacity of points in scatter plots.
+#' @param fits whether to include fits in scatter plots.
+#' @param colours vector of colours to use for each dataset.
#'
#' @details
#' The returned list has three items:
@@ -44,14 +48,25 @@
#' names(comparison)
#' names(comparison$Plots)
#' @importFrom ggplot2 ggplot aes_string geom_point geom_smooth geom_boxplot
-#' geom_violin scale_y_continuous scale_y_log10 scale_x_log10 xlab ylab ggtitle
-#' theme_minimal
+#' scale_y_continuous scale_y_log10 scale_x_log10 xlab ylab ggtitle
+#' theme_minimal scale_colour_manual scale_fill_manual
#' @importFrom scater cpm<-
#' @export
-compareSCESets <- function(sces) {
+compareSCESets <- function(sces, point.size = 0.1, point.alpha = 0.1,
+ fits = TRUE, colours = NULL) {
checkmate::assertList(sces, types = "SCESet", any.missing = FALSE,
min.len = 1, names = "unique")
+ checkmate::assertNumber(point.size, finite = TRUE)
+ checkmate::assertNumber(point.alpha, lower = 0, upper = 1)
+ checkmate::assertLogical(fits, any.missing = FALSE, len = 1)
+
+ if (!is.null(colours)) {
+ checkmate::assertCharacter(colours, any.missing = FALSE,
+ len = length(sces))
+ } else {
+ colours <- scales::hue_pal()(length(sces))
+ }
for (name in names(sces)) {
sce <- sces[[name]]
@@ -84,25 +99,27 @@ compareSCESets <- function(sces) {
colour = "Dataset")) +
#geom_violin(draw_quantiles = c(0.25, 0.5, 0.75)) +
geom_boxplot() +
+ scale_colour_manual(values = colours) +
ylab(expression(paste("Mean ", log[2], "(CPM + 1)"))) +
ggtitle("Distribution of mean expression") +
theme_minimal()
vars <- ggplot(fData.all,
- aes_string(x = "Dataset", y = "VarCPM",
+ aes_string(x = "Dataset", y = "VarLogCPM",
colour = "Dataset")) +
#geom_violin(draw_quantiles = c(0.25, 0.5, 0.75)) +
geom_boxplot() +
- scale_y_log10(labels = scales::comma) +
- ylab("CPM Variance") +
+ scale_colour_manual(values = colours) +
+ ylab(expression(paste("Variance ", log[2], "(CPM + 1)"))) +
ggtitle("Distribution of variance") +
theme_minimal()
mean.var <- ggplot(fData.all,
aes_string(x = "MeanLogCPM", y = "VarLogCPM",
colour = "Dataset", fill = "Dataset")) +
- geom_point(size = 0.1, alpha = 0.1) +
- geom_smooth() +
+ geom_point(size = point.size, alpha = point.alpha) +
+ scale_colour_manual(values = colours) +
+ scale_fill_manual(values = colours) +
xlab(expression(paste("Mean ", log[2], "(CPM + 1)"))) +
ylab(expression(paste("Variance ", log[2], "(CPM + 1)"))) +
ggtitle("Mean-variance relationship") +
@@ -113,6 +130,7 @@ compareSCESets <- function(sces) {
colour = "Dataset")) +
geom_boxplot() +
scale_y_continuous(labels = scales::comma) +
+ scale_colour_manual(values = colours) +
ylab("Total counts per cell") +
ggtitle("Distribution of library sizes") +
theme_minimal()
@@ -122,6 +140,7 @@ compareSCESets <- function(sces) {
colour = "Dataset")) +
geom_boxplot() +
scale_y_continuous(limits = c(0, 100)) +
+ scale_colour_manual(values = colours) +
ylab("Percentage zeros per gene") +
ggtitle("Distribution of zeros per gene") +
theme_minimal()
@@ -131,6 +150,7 @@ compareSCESets <- function(sces) {
colour = "Dataset")) +
geom_boxplot() +
scale_y_continuous(limits = c(0, 100)) +
+ scale_colour_manual(values = colours) +
ylab("Percentage zeros per cell") +
ggtitle("Distribution of zeros per cell") +
theme_minimal()
@@ -138,14 +158,20 @@ compareSCESets <- function(sces) {
mean.zeros <- ggplot(fData.all,
aes_string(x = "MeanCounts", y = "pct_dropout",
colour = "Dataset", fill = "Dataset")) +
- geom_point(size = 0.1, alpha = 0.1) +
- geom_smooth() +
+ geom_point(size = point.size, alpha = point.alpha) +
scale_x_log10(labels = scales::comma) +
+ scale_colour_manual(values = colours) +
+ scale_fill_manual(values = colours) +
xlab("Mean count") +
ylab("Percentage zeros") +
ggtitle("Mean-dropout relationship") +
theme_minimal()
+ if (fits) {
+ mean.var <- mean.var + geom_smooth()
+ mean.zeros <- mean.zeros + geom_smooth()
+ }
+
comparison <- list(FeatureData = fData.all,
PhenoData = pData.all,
Plots = list(Means = means,
@@ -166,6 +192,10 @@ compareSCESets <- function(sces) {
#'
#' @param sces named list of SCESet objects to combine and compare.
#' @param ref string giving the name of the SCESet to use as the reference
+#' @param point.size size of points in scatter plots.
+#' @param point.alpha opacity of points in scatter plots.
+#' @param fits whether to include fits in scatter plots.
+#' @param colours vector of colours to use for each dataset.
#'
#' @details
#'
@@ -225,19 +255,31 @@ compareSCESets <- function(sces) {
#' names(difference)
#' names(difference$Plots)
#' @importFrom ggplot2 ggplot aes_string geom_point geom_boxplot xlab ylab
-#' ggtitle theme_minimal geom_hline geom_abline
+#' ggtitle theme_minimal geom_hline geom_abline scale_colour_manual
+#' scale_fill_manual
#' @importFrom scater cpm<-
#' @export
-diffSCESets <- function(sces, ref) {
+diffSCESets <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
+ fits = TRUE, colours = NULL) {
checkmate::assertList(sces, types = "SCESet", any.missing = FALSE,
min.len = 2, names = "unique")
checkmate::assertString(ref)
+ checkmate::assertNumber(point.size, finite = TRUE)
+ checkmate::assertNumber(point.alpha, lower = 0, upper = 1)
+ checkmate::assertLogical(fits, any.missing = FALSE, len = 1)
if (!(ref %in% names(sces))) {
stop("'ref' must be the name of an SCESet in 'sces'")
}
+ if (!is.null(colours)) {
+ checkmate::assertCharacter(colours, any.missing = FALSE,
+ len = length(sces) - 1)
+ } else {
+ colours <- scales::hue_pal()(length(sces))
+ }
+
ref.dim <- dim(sces[[ref]])
for (name in names(sces)) {
@@ -314,6 +356,7 @@ diffSCESets <- function(sces, ref) {
colour = "Dataset")) +
geom_hline(yintercept = 0, colour = "red") +
geom_boxplot() +
+ scale_colour_manual(values = colours) +
ylab(expression(paste("Rank difference mean ", log[2], "(CPM + 1)"))) +
ggtitle("Difference in mean expression") +
theme_minimal()
@@ -323,6 +366,7 @@ diffSCESets <- function(sces, ref) {
colour = "Dataset")) +
geom_hline(yintercept = 0, colour = "red") +
geom_boxplot() +
+ scale_colour_manual(values = colours) +
ylab(expression(paste("Rank difference variance ", log[2],
"(CPM + 1)"))) +
ggtitle("Difference in variance") +
@@ -330,9 +374,11 @@ diffSCESets <- function(sces, ref) {
mean.var <- ggplot(fData.all,
aes_string(x = "exprs_rank", y = "MeanRankVarDiff",
- colour = "Dataset")) +
+ colour = "Dataset", fill = "Dataset")) +
geom_hline(yintercept = 0, colour = "red") +
- geom_point() +
+ geom_point(size = point.size, alpha = point.alpha) +
+ scale_colour_manual(values = colours) +
+ scale_fill_manual(values = colours) +
xlab("Expression rank") +
ylab(expression(paste("Difference in variance ", log[2],
"(CPM + 1)"))) +
@@ -344,6 +390,7 @@ diffSCESets <- function(sces, ref) {
colour = "Dataset")) +
geom_hline(yintercept = 0, colour = "red") +
geom_boxplot() +
+ scale_colour_manual(values = colours) +
ylab(paste("Rank difference libray size")) +
ggtitle("Difference in library sizes") +
theme_minimal()
@@ -353,6 +400,7 @@ diffSCESets <- function(sces, ref) {
colour = "Dataset")) +
geom_hline(yintercept = 0, colour = "red") +
geom_boxplot() +
+ scale_colour_manual(values = colours) +
ylab(paste("Rank difference percentage zeros")) +
ggtitle("Difference in zeros per gene") +
theme_minimal()
@@ -362,15 +410,18 @@ diffSCESets <- function(sces, ref) {
colour = "Dataset")) +
geom_hline(yintercept = 0, colour = "red") +
geom_boxplot() +
+ scale_colour_manual(values = colours) +
ylab(paste("Rank difference percentage zeros")) +
ggtitle("Difference in zeros per cell") +
theme_minimal()
mean.zeros <- ggplot(fData.all,
aes_string(x = "exprs_rank", y = "MeanRankZerosDiff",
- colour = "Dataset")) +
+ colour = "Dataset", fill = "Dataset")) +
geom_hline(yintercept = 0, colour = "red") +
- geom_point() +
+ geom_point(size = point.size, alpha = point.alpha) +
+ scale_colour_manual(values = colours) +
+ scale_fill_manual(values = colours) +
xlab("Expression rank") +
ylab("Difference in percentage zeros per gene") +
ggtitle("Difference in mean-zeros relationship") +
@@ -380,7 +431,8 @@ diffSCESets <- function(sces, ref) {
aes_string(x = "RefRankMeanLogCPM", y = "MeanLogCPM",
colour = "Dataset")) +
geom_abline(intercept = 0, slope = 1, colour = "red") +
- geom_point() +
+ geom_point(size = point.size, alpha = point.alpha) +
+ scale_colour_manual(values = colours) +
xlab(expression(paste("Reference mean ", log[2], "(CPM + 1)"))) +
ylab(expression(paste("Alternative mean ", log[2], "(CPM + 1)"))) +
ggtitle("Ranked means") +
@@ -390,7 +442,8 @@ diffSCESets <- function(sces, ref) {
aes_string(x = "RefRankVarLogCPM", y = "VarLogCPM",
colour = "Dataset")) +
geom_abline(intercept = 0, slope = 1, colour = "red") +
- geom_point() +
+ geom_point(size = point.size, alpha = point.alpha) +
+ scale_colour_manual(values = colours) +
xlab(expression(paste("Reference variance ", log[2], "(CPM + 1)"))) +
ylab(expression(paste("Alternative variance ", log[2], "(CPM + 1)"))) +
ggtitle("Ranked variances") +
@@ -400,7 +453,8 @@ diffSCESets <- function(sces, ref) {
aes_string(x = "RefRankLibSize", y = "total_counts",
colour = "Dataset")) +
geom_abline(intercept = 0, slope = 1, colour = "red") +
- geom_point() +
+ geom_point(size = point.size, alpha = point.alpha) +
+ scale_colour_manual(values = colours) +
xlab("Reference library size") +
ylab("Alternative library size") +
ggtitle("Ranked library sizes") +
@@ -410,7 +464,8 @@ diffSCESets <- function(sces, ref) {
aes_string(x = "RefRankZeros", y = "pct_dropout",
colour = "Dataset")) +
geom_abline(intercept = 0, slope = 1, colour = "red") +
- geom_point() +
+ geom_point(size = point.size, alpha = point.alpha) +
+ scale_colour_manual(values = colours) +
xlab("Reference percentage zeros") +
ylab("Alternative percentage zeros") +
ggtitle("Ranked percentage zeros per gene") +
@@ -420,12 +475,18 @@ diffSCESets <- function(sces, ref) {
aes_string(x = "RefRankZeros", y = "pct_dropout",
colour = "Dataset")) +
geom_abline(intercept = 0, slope = 1, colour = "red") +
- geom_point() +
+ geom_point(size = point.size, alpha = point.alpha) +
+ scale_colour_manual(values = colours) +
xlab("Reference percentage zeros") +
ylab("Alternative percentage zeros") +
ggtitle("Ranked percentage zeros per cell") +
theme_minimal()
+ if (fits) {
+ mean.var <- mean.var + geom_smooth()
+ mean.zeros <- mean.zeros + geom_smooth()
+ }
+
comparison <- list(Reference = ref.sce,
FeatureData = fData.all,
PhenoData = pData.all,
@@ -444,3 +505,282 @@ diffSCESets <- function(sces, ref) {
return(comparison)
}
+
+#' Make comparison panel
+#'
+#' Combine the plots from \code{compareSCESets} into a single panel.
+#'
+#' @param comp list returned by \code{\link{compareSCESets}}.
+#' @param title title for the panel.
+#' @param labels vector of labels for each of the seven plots.
+#'
+#' @return Combined panel plot
+#'
+#' @examples
+#' \dontrun{
+#' sim1 <- splatSimulate(nGenes = 1000, groupCells = 20)
+#' sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
+#' comparison <- compareSCESets(list(Splat = sim1, Simple = sim2))
+#' panel <- makeCompPanel(comparison)
+#' }
+#'
+#' @importFrom ggplot2 theme element_blank
+#' @export
+makeCompPanel <- function(comp, title = "Comparison",
+ labels = c("Means", "Variance",
+ "Mean-variance relationship",
+ "Library size", "Zeros per gene",
+ "Zeros per cell",
+ "Mean-zeros relationship")) {
+
+ if (!requireNamespace("cowplot", quietly = TRUE)) {
+ stop("The `cowplot` package is required to make panels.")
+ }
+
+ checkmate::assertList(comp, any.missing = FALSE, len = 3)
+ checkmate::checkString(title)
+ checkmate::checkCharacter(labels, len = 7)
+
+ plots <- list(p1 = comp$Plots$Means, p2 = comp$Plots$Variances,
+ p3 = comp$Plots$MeanVar, p4 = comp$Plots$LibrarySizes,
+ p5 = comp$Plots$ZerosGene, p6 = comp$Plots$ZerosCell,
+ p7 = comp$Plots$MeanZeros)
+
+ # Remove titles and legends
+ for (plot in names(plots)) {
+ plots[[plot]] <- plots[[plot]] + theme(legend.position = "none",
+ plot.title = element_blank())
+ }
+
+ # Remove x-axis title from some plots
+ for (plot in paste0("p", c(1, 2, 4, 5, 6))) {
+ plots[[plot]] <- plots[[plot]] + theme(axis.title.x = element_blank())
+ }
+
+ plots$leg <- cowplot::get_legend(plots$p1 +
+ theme(legend.position = "bottom"))
+
+ panel <- cowplot::ggdraw() +
+ cowplot::draw_label(title, 0.5, 0.98,
+ fontface = "bold", size = 18) +
+ cowplot::draw_label(labels[1], 0.01, 0.95,
+ fontface = "bold", hjust = 0, vjust = 0) +
+ cowplot::draw_plot(plots$p1, 0.0, 0.74, 0.5, 0.20) +
+ cowplot::draw_label(labels[2], 0.51, 0.95,
+ fontface = "bold", hjust = 0, vjust = 0) +
+ cowplot::draw_plot(plots$p2, 0.5, 0.74, 0.5, 0.20) +
+ cowplot::draw_label(labels[3], 0.01, 0.70,
+ fontface = "bold", hjust = 0, vjust = 0) +
+ cowplot::draw_plot(plots$p3, 0.0, 0.49, 0.5, 0.20) +
+ cowplot::draw_label(labels[4], 0.51, 0.70,
+ fontface = "bold", hjust = 0, vjust = 0) +
+ cowplot::draw_plot(plots$p4, 0.5, 0.49, 0.5, 0.20) +
+ cowplot::draw_label(labels[5], 0.01, 0.45,
+ fontface = "bold", hjust = 0, vjust = 0) +
+ cowplot::draw_plot(plots$p5, 0.0, 0.24, 0.5, 0.20) +
+ cowplot::draw_label(labels[6], 0.51, 0.45,
+ fontface = "bold", hjust = 0, vjust = 0) +
+ cowplot::draw_plot(plots$p6, 0.5, 0.24, 0.5, 0.20) +
+ cowplot::draw_label(labels[7], 0.01, 0.21,
+ fontface = "bold", hjust = 0, vjust = 0) +
+ cowplot::draw_plot(plots$p7, 0.0, 0.00, 0.5, 0.20) +
+ cowplot::draw_plot(plots$leg, 0.5, 0.00, 0.5, 0.20)
+
+ return(panel)
+}
+
+
+#' Make difference panel
+#'
+#' Combine the plots from \code{diffSCESets} into a single panel.
+#'
+#' @param diff list returned by \code{\link{diffSCESets}}.
+#' @param title title for the panel.
+#' @param labels vector of labels for each of the seven sections.
+#'
+#' @return Combined panel plot
+#'
+#' @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)
+#' }
+#'
+#' @importFrom ggplot2 theme element_blank
+#' @export
+makeDiffPanel <- function(diff, title = "Difference comparison",
+ labels = c("Means", "Variance", "Library size",
+ "Zeros per cell", "Zeros per gene",
+ "Mean-variance relationship",
+ "Mean-zeros relationship")) {
+
+ if (!requireNamespace("cowplot", quietly = TRUE)) {
+ stop("The `cowplot` package is required to make panels.")
+ }
+
+ checkmate::assertList(diff, any.missing = FALSE, len = 5)
+ checkmate::checkString(title)
+ checkmate::checkCharacter(labels, len = 7)
+
+ plots <- list(p1 = diff$Plots$Means, p2 = diff$QQPlots$Means,
+ p3 = diff$Plots$Variances, p4 = diff$QQPlots$Variances,
+ p5 = diff$Plots$MeanVar, p6 = diff$Plots$LibrarySizes,
+ p7 = diff$QQPlots$LibrarySizes, p8 = diff$Plots$ZerosCell,
+ p9 = diff$QQPlots$ZerosCell, p10 = diff$Plots$ZerosGene,
+ p11 = diff$QQPlots$ZerosGene, p12 = diff$Plots$MeanZeros)
+
+ # Remove titles and legends
+ for (plot in names(plots)) {
+ plots[[plot]] <- plots[[plot]] + theme(legend.position = "none",
+ plot.title = element_blank())
+ }
+
+ # Remove x-axis title from some plots
+ for (plot in paste0("p", c(1, 3, 6, 8, 10))) {
+ plots[[plot]] <- plots[[plot]] + theme(axis.title.x = element_blank())
+ }
+
+ plots$leg <- cowplot::get_legend(plots$p1 +
+ theme(legend.position = "bottom"))
+
+ panel <- cowplot::ggdraw() +
+ cowplot::draw_label(title, 0.5, 0.98,
+ fontface = "bold", size = 18) +
+ cowplot::draw_label(labels[1], 0.0, 0.94,
+ fontface = "bold", hjust = 0, vjust = 0) +
+ cowplot::draw_plot(plots$p1, 0.0, 0.64, 0.18, 0.29) +
+ cowplot::draw_plot(plots$p2, 0.0, 0.32, 0.18, 0.29) +
+ cowplot::draw_label(labels[2], 0.21, 0.94,
+ fontface = "bold", hjust = 0, vjust = 0) +
+ cowplot::draw_plot(plots$p3, 0.21, 0.64, 0.18, 0.29) +
+ cowplot::draw_plot(plots$p4, 0.21, 0.32, 0.18, 0.29) +
+ cowplot::draw_label(labels[6], 0.0, 0.30,
+ fontface = "bold", hjust = 0, vjust = 0) +
+ cowplot::draw_plot(plots$p5, 0.0, 0.0, 0.38, 0.29) +
+ cowplot::draw_label(labels[3], 0.41, 0.94,
+ fontface = "bold", hjust = 0, vjust = 0) +
+ cowplot::draw_plot(plots$p6, 0.41, 0.64, 0.18, 0.29) +
+ cowplot::draw_plot(plots$p7, 0.41, 0.32, 0.18, 0.29) +
+ cowplot::draw_label(labels[4], 0.61, 0.94,
+ fontface = "bold", hjust = 0, vjust = 0) +
+ cowplot::draw_plot(plots$p8, 0.61, 0.64, 0.18, 0.29) +
+ cowplot::draw_plot(plots$p9, 0.61, 0.32, 0.18, 0.29) +
+ cowplot::draw_label(labels[7], 0.41, 0.30,
+ fontface = "bold", hjust = 0, vjust = 0) +
+ cowplot::draw_plot(plots$p12, 0.41, 0.0, 0.38, 0.29) +
+ cowplot::draw_label(labels[5], 0.81, 0.94,
+ fontface = "bold", hjust = 0, vjust = 0) +
+ cowplot::draw_plot(plots$p10, 0.81, 0.64, 0.18, 0.29) +
+ cowplot::draw_plot(plots$p11, 0.81, 0.32, 0.18, 0.29) +
+ cowplot::draw_plot(plots$leg, 0.81, 0.0, 0.2, 0.29)
+
+ return(panel)
+}
+
+
+#' Make overall panel
+#'
+#' Combine the plots from \code{compSCESets} and \code{diffSCESets} into a
+#' single panel.
+#'
+#' @param comp list returned by \code{\link{compareSCESets}}.
+#' @param diff list returned by \code{\link{diffSCESets}}.
+#' @param title title for the panel.
+#' @param row.labels vector of labels for each of the seven rows.
+#'
+#' @return Combined panel plot
+#'
+#' @examples
+#' \dontrun{
+#' sim1 <- splatSimulate(nGenes = 1000, groupCells = 20)
+#' sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
+#' comparison <- compSCESets(list(Splat = sim1, Simple = sim2))
+#' difference <- diffSCESets(list(Splat = sim1, Simple = sim2), ref = "Simple")
+#' panel <- makeOverallPanel(comparison, difference)
+#' }
+#'
+#' @importFrom ggplot2 theme element_blank
+#' @export
+makeOverallPanel <- function(comp, diff, title = "Overall comparison",
+ row.labels = c("Means", "Variance",
+ "Mean-variance relationship",
+ "Library size", "Zeros per cell",
+ "Zeros per gene",
+ "Mean-zeros relationship")) {
+
+ if (!requireNamespace("cowplot", quietly = TRUE)) {
+ stop("The `cowplot` package is required to make panels.")
+ }
+
+ checkmate::assertList(comp, any.missing = FALSE, len = 3)
+ checkmate::assertList(diff, any.missing = FALSE, len = 5)
+ checkmate::checkString(title)
+ checkmate::checkCharacter(row.labels, len = 7)
+
+ plots <- list(p1 = comp$Plots$Means, p2 = diff$Plots$Means,
+ p3 = diff$QQPlots$Means, p4 = comp$Plots$Variances,
+ p5 = diff$Plots$Variances, p6 = diff$QQPlots$Variances,
+ p7 = comp$Plots$MeanVar, p8 = diff$Plots$MeanVar,
+ p9 = comp$Plots$LibrarySizes, p10 = diff$Plots$LibrarySizes,
+ p11 = diff$QQPlots$LibrarySizes, p12 = comp$Plots$ZerosCell,
+ p13 = diff$Plots$ZerosCell, p14 = diff$QQPlots$ZerosCell,
+ p15 = comp$Plots$ZerosGene, p16 = diff$Plots$ZerosGene,
+ p17 = diff$QQPlots$ZerosGene, p18 = comp$Plots$MeanZeros,
+ p19 = diff$Plots$MeanZeros)
+
+ # Remove titles and legends
+ for (plot in names(plots)) {
+ plots[[plot]] <- plots[[plot]] + theme(legend.position = "none",
+ plot.title = element_blank())
+ }
+
+ # Remove x-axis title from some plots
+ for (plot in paste0("p", c(1, 2, 4, 5, 9, 10, 12, 13, 15, 16))) {
+ plots[[plot]] <- plots[[plot]] + theme(axis.title.x = element_blank())
+ }
+
+ plots$leg <- cowplot::get_legend(plots$p1 +
+ theme(legend.position = "bottom"))
+
+ panel <- cowplot::ggdraw() +
+ cowplot::draw_label(title, 0.5, 0.995,
+ fontface = "bold", size = 18) +
+ cowplot::draw_label(row.labels[1], 0.01, 0.985,
+ fontface = "bold", hjust = 0, vjust = 0) +
+ cowplot::draw_plot(plots$p1, 0.00, 0.86, 0.32, 0.12) +
+ cowplot::draw_plot(plots$p2, 0.34, 0.86, 0.32, 0.12) +
+ cowplot::draw_plot(plots$p3, 0.67, 0.86, 0.32, 0.12) +
+ cowplot::draw_label(row.labels[2], 0.01, 0.845,
+ fontface = "bold", hjust = 0, vjust = 0) +
+ cowplot::draw_plot(plots$p4, 0.00, 0.72, 0.32, 0.12) +
+ cowplot::draw_plot(plots$p5, 0.34, 0.72, 0.32, 0.12) +
+ cowplot::draw_plot(plots$p6, 0.67, 0.72, 0.32, 0.12) +
+ cowplot::draw_label(row.labels[3], 0.01, 0.705,
+ fontface = "bold", hjust = 0, vjust = 0) +
+ cowplot::draw_plot(plots$p7, 0.00, 0.58, 0.49, 0.12) +
+ cowplot::draw_plot(plots$p8, 0.51, 0.58, 0.49, 0.12) +
+ cowplot::draw_label(row.labels[4], 0.01, 0.56,
+ fontface = "bold", hjust = 0, vjust = 0) +
+ cowplot::draw_plot(plots$p9, 0.00, 0.44, 0.32, 0.12) +
+ cowplot::draw_plot(plots$p10, 0.34, 0.44, 0.32, 0.12) +
+ cowplot::draw_plot(plots$p11, 0.67, 0.44, 0.32, 0.12) +
+ cowplot::draw_label(row.labels[5], 0.01, 0.425,
+ fontface = "bold", hjust = 0, vjust = 0) +
+ cowplot::draw_plot(plots$p12, 0.00, 0.30, 0.32, 0.12) +
+ cowplot::draw_plot(plots$p13, 0.34, 0.30, 0.32, 0.12) +
+ cowplot::draw_plot(plots$p14, 0.67, 0.30, 0.32, 0.12) +
+ cowplot::draw_label(row.labels[6], 0.01, 0.285,
+ fontface = "bold", hjust = 0, vjust = 0) +
+ cowplot::draw_plot(plots$p15, 0.00, 0.16, 0.32, 0.12) +
+ cowplot::draw_plot(plots$p16, 0.34, 0.16, 0.32, 0.12) +
+ cowplot::draw_plot(plots$p17, 0.67, 0.16, 0.32, 0.12) +
+ cowplot::draw_label(row.labels[7], 0.01, 0.145,
+ fontface = "bold", hjust = 0, vjust = 0) +
+ cowplot::draw_plot(plots$p18, 0.00, 0.02, 0.49, 0.12) +
+ cowplot::draw_plot(plots$p19, 0.51, 0.02, 0.49, 0.12) +
+ cowplot::draw_plot(plots$leg, 0.00, 0.00, 1.00, 0.02)
+
+ return(panel)
+}
diff --git a/man/compareSCESets.Rd b/man/compareSCESets.Rd
index e0533d3114487674ac807388762d2e1f1c41cb28..9121d6ea357da34aa8cde8008e767731b5a567f4 100644
--- a/man/compareSCESets.Rd
+++ b/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.
diff --git a/man/diffSCESets.Rd b/man/diffSCESets.Rd
index 3fc3e60bcb04fb6ca0ed1de07fe9d8439fc48e20..529b43468c8216263c72cbf5ebd1405a7cbf7b55 100644
--- a/man/diffSCESets.Rd
+++ b/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.
diff --git a/man/makeCompPanel.Rd b/man/makeCompPanel.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..1e32fb056211fa791e114c1ffeb0f4d4c46a115e
--- /dev/null
+++ b/man/makeCompPanel.Rd
@@ -0,0 +1,32 @@
+% 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)
+}
+
+}
diff --git a/man/makeDiffPanel.Rd b/man/makeDiffPanel.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..10b6f6ba47b3bdef19146808519aafa823172db1
--- /dev/null
+++ b/man/makeDiffPanel.Rd
@@ -0,0 +1,32 @@
+% 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)
+}
+
+}
diff --git a/man/makeOverallPanel.Rd b/man/makeOverallPanel.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..9e97e5cba3364444efea868b4ab2cb9c2d059851
--- /dev/null
+++ b/man/makeOverallPanel.Rd
@@ -0,0 +1,37 @@
+% 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)
+}
+
+}
diff --git a/vignettes/splatter.Rmd b/vignettes/splatter.Rmd
index 376ba8c104ecb87ddb4e36679b9b77b7e0f573b1..7d728abf8869c5d779c9e7ba950ff7babbe54a78 100644
--- a/vignettes/splatter.Rmd
+++ b/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}