Readme updated (45ebb64c) · Commits · github_fork / Plot1cell

R/plot_violin.R

+24 −15

Original line number	Diff line number	Diff line
		@@ -9,7 +9,7 @@
		#'
		#' @param seu_obj A complete Seurat object
		#' @param feature Gene name. Only one gene is allowed.
		#' @param cell.types Cell types of interest. By default, all cell types are included.
		#' @param celltypes Cell types of interest. By default, all cell types are included.
		#' @param groups Groups selected for plotting. Support multiple groups.
		#' @param add.dot Whether or not to add points on the violins.
		#' @param font.size Font size for the labels.
		@@ -21,23 +21,32 @@
		complex_vlnplot_single <- function(
		seu_obj,
		feature,
		cell.types=NULL,
		celltypes=NULL,
		groups,
		add.dot = T,
		font.size=14,
		pt.size=0.1,
		split.by=NULL
		){
		if(is.null(cell.types)){
		cell.types = levels(seu_obj)
		if(is.null(celltypes)){
		celltypes = levels(seu_obj)
		}
		gene_count<-extract_gene_count(seu_obj=seu_obj, features = feature, cell.types = celltypes, meta.groups = c(groups, split.by))
		allgroups<-c(groups,split.by )
		for(i in 1:length(allgroups)){
		if (is.null(levels(seu_obj@meta.data[,allgroups[i]]))){
		seu_obj@meta.data[,allgroups[i]] <-factor(seu_obj@meta.data[,allgroups[i]], levels = names(table(seu_obj@meta.data[,allgroups[i]])))
		}
		group_level<-levels(seu_obj@meta.data[,allgroups[i]])
		gene_count[,allgroups[i]]<-factor(gene_count[,allgroups[i]],
		levels = group_level)
		}
		gene_count<-extract_gene_count(seu_obj=seu_obj, features = feature, cell.types = cell.types, meta.groups = c(groups, split.by))
		max_exp<-max(gene_count[,feature])
		set.seed(seed = 42)
		noise <- rnorm(n = length(x = gene_count[,feature])) / 100000
		gene_count[, feature]<-gene_count[,feature]+noise
		if (length(groups)==1) {
		if(length(cell.types)==1){
		if(length(celltypes)==1){
		p<-ggplot(gene_count, aes_string(x=groups, y=feature, fill=groups))+
		geom_violin(scale = 'width', adjust = 1, trim = TRUE, size=0.3, alpha=0.5, color="pink")+
		xlab("") + ylab("") + ggtitle(feature) +
		@@ -59,7 +68,7 @@ complex_vlnplot_single <- function(
		strip_t <- which(grepl('strip-t', g$layout$name))
		strip_r <- which(grepl('strip-r', g$layout$name))
		strip_both<-c( strip_r,strip_t)
		ncol <- length(cell.types) + length(names(table(gene_count[,split.by])))
		ncol <- length(celltypes) + length(names(table(gene_count[,split.by])))
		fills <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(12, "Set3"))(ncol)
		k <- 1
		for (i in strip_both) {
		@@ -74,11 +83,11 @@ complex_vlnplot_single <- function(
		} else {
		if(is.null(split.by)){
		plot_list<-list()
		for(i in 1:length(cell.types)){
		cell_count <- gene_count[gene_count$celltype==cell.types[i],]
		for(i in 1:length(celltypes)){
		cell_count <- gene_count[gene_count$celltype==celltypes[i],]
		p<-ggplot(cell_count, aes_string(x=groups, y=feature, fill=groups))+
		geom_violin(scale = 'width', adjust = 1, trim = TRUE, size=0.3, alpha=0.5, color="pink")+
		xlab("") + ylab(cell.types[i]) +
		xlab("") + ylab(celltypes[i]) +
		theme(panel.background = element_rect(fill = "white",colour = "black"),
		legend.position = "none",
		axis.text.x = element_blank(),
		@@ -115,7 +124,7 @@ complex_vlnplot_single <- function(
		strip_t <- which(grepl('strip-t', g$layout$name))
		strip_r <- which(grepl('strip-r', g$layout$name))
		strip_both<-c(strip_t, strip_r)
		ncol <- length(cell.types) + length(names(table(gene_count[,split.by])))
		ncol <- length(celltypes) + length(names(table(gene_count[,split.by])))
		fills <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(12, "Set3"))(ncol)
		k <- 1
		for (i in strip_both) {
		@@ -130,7 +139,7 @@ complex_vlnplot_single <- function(
		if(!is.null(split.by)){
		stop("This function does not support spliting multiple groups. Plots will look too messy! Please select one group only in the 'groups' parameter if you want to use 'split.by'.")
		}
		if(length(cell.types)==1){
		if(length(celltypes)==1){
		gene_count<-melt(gene_count[,c(feature, groups)], measure.vars = groups)
		p<-ggplot(gene_count, aes_string(x="value", y=feature, fill="value"))+
		geom_violin(scale = 'width', adjust = 1, trim = TRUE, size=0.3, alpha=0.5, color="pink")+
		@@ -154,11 +163,11 @@ complex_vlnplot_single <- function(
		for(i in 1:length(groups)){
		group=groups[i]
		cell_count<-gene_count[,c(feature, group, "celltype")]
		for(j in 1:length(cell.types)){
		cell_count2 <- cell_count[cell_count$celltype==cell.types[j],]
		for(j in 1:length(celltypes)){
		cell_count2 <- cell_count[cell_count$celltype==celltypes[j],]
		p<-ggplot(cell_count2, aes_string(x=group, y=feature, fill=group))+
		geom_violin(scale = 'width', adjust = 1, trim = TRUE, size=0.3, alpha=0.5, color="pink")+
		xlab("") + ylab(cell.types[j]) +
		xlab("") + ylab(celltypes[j]) +
		theme(panel.background = element_rect(fill = "white",colour = "black"),
		legend.position = "none",
		axis.text.x = element_blank(),

README.html

+26 −4

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README.md

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		@@ -56,9 +56,28 @@ dev.off()
		```
		![alt text](https://github.com/HaojiaWu/Plot1cell/blob/master/dotplot_multiple.png) <br />

		### 3. Vlnplot to show gene expression across groups
		### 3. Violin plot to show gene expression across groups
		#### One gene/one group violin plot:
		```
		png(filename = 'vlnplot_single.png', width = 4, height = 6,units = 'in', res = 300)
		complex_vlnplot_single(iri.integrated, feature = "Havcr1", groups = "Group",celltypes = c("PTS1" , "PTS2" , "PTS3" , "NewPT1" , "NewPT2"))
		dev.off()
		```
		![alt text](https://github.com/HaojiaWu/Plot1cell/blob/master/vlnplot_single.png) <br />

		#### One genes/multiple groups violin plot:
		```
		png(filename = 'vlnplot_multiple.png', width = 8, height = 6,units = 'in', res = 300)
		complex_vlnplot_single(iri.integrated, feature = "Havcr1", groups = c("Group","Replicates"),celltypes = c("PTS1" , "PTS2" , "PTS3" , "NewPT1" , "NewPT2"))
		dev.off()
		```
		![alt text](https://github.com/HaojiaWu/Plot1cell/blob/master/vlnplot_multiple.png) <br />

		Note that the Replicates group here is for demo purpose. This is not the mouse ID as reported in our original paper.

		#### Multiple genes/multiple groups.
		The violin plot will look too messy in this scenario so it is not included in plot1cell. It would highly recommend to use the complex_dot_plot instead. <br />
		For scRNA-seq studies with higher complexity, the complex_vlnplot_single function also allows split the group by another group in the meta data with the argument "split.by". Since the demo dataset doesn't have this complexity, examples are not included here. Users can refer to our recent DKD dataset with multiple treatments/two timepoints (the PCT violin graph in <a href="https://humphreyslab.com/SingleCell/">K.I.T.</a>)

man/complex_vlnplot_single.Rd

+2 −2

Original line number	Diff line number	Diff line
		@@ -7,7 +7,7 @@
		complex_vlnplot_single(
		seu_obj,
		feature,
		cell.types = NULL,
		celltypes = NULL,
		groups,
		add.dot = T,
		font.size = 14,
		@@ -20,7 +20,7 @@ complex_vlnplot_single(

		\item{feature}{Gene name. Only one gene is allowed.}

		\item{cell.types}{Cell types of interest. By default, all cell types are included.}
		\item{celltypes}{Cell types of interest. By default, all cell types are included.}

		\item{groups}{Groups selected for plotting. Support multiple groups.}

vlnplot_multiple.png

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+310 KiB

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