fix plot (d1eaed16) · Commits · github_fork / Plot1cell

R/plot_umap.R

+18 −12

Original line number	Diff line number	Diff line
		@@ -6,12 +6,14 @@
		#' This function can be used for plotting a single gene or multiple genes expression across
		#' different groups in a seurat featureplot format.
		#'
		#' @param seu_obj A complete Seurat object
		#' @param seu_obj A complete Seurat object.
		#' @param features Gene names to be plotted.
		#' @param group The group to show on y axis. One of the column names in meta.data.
		#' @param select Select the elements within the group to show.
		#' @param cols Change the color legend.
		#' @param label.size Change the label size.
		#' @param strip.color Colors for the strip background.
		#' @param pt.size Point size for each cell.
		#' @return A ggplot object
		#' @export

		@@ -21,8 +23,10 @@ complex_featureplot<-function(
		group,
		select = NULL,
		cols = NULL,
		label.size=14,
		order=F
		label.size = 12,
		order = F,
		strip.color = NULL,
		pt.size = 0.01
		){
		gene_count<-extract_gene_count(seu_obj,features = features, meta.groups = group)
		if (is.null(levels(seu_obj@meta.data[,group]))){
		@@ -51,12 +55,12 @@ complex_featureplot<-function(
		df_all$gene<-factor(df_all$gene, levels=features)
		if(order){
		df_all$isExpr<-ifelse(df_all$Exp>0, "Yes", "NO")
		p<-ggplot(df_all, aes(UMAP1, UMAP2))+geom_point(color="gray80",size=0.01)+
		geom_point(data = df_all[df_all$isExpr=="Yes",], aes(UMAP1, UMAP2, color=Exp), size=0.01)
		p<-ggplot(df_all, aes(UMAP1, UMAP2))+geom_point(color="gray80",size=pt.size)+
		geom_point(data = df_all[df_all$isExpr=="Yes",], aes(UMAP1, UMAP2, color=Exp), size=pt.size)
		} else {
		p<-ggplot(df_all, aes(UMAP1, UMAP2, color=Exp))+geom_point(size=0.01)
		p<-ggplot(df_all, aes(UMAP1, UMAP2, color=Exp))+geom_point(size=pt.size)
		}
		p +
		p<-p +
		scale_color_gradientn(colours = cols,
		na.value = "white", limits=c(quantile(df_all$Exp, 0,na.rm= T), quantile(df_all$Exp, 1,na.rm= T)),
		breaks = c(quantile(df_all$Exp, 0,na.rm= T), quantile(df_all$Exp, 1,na.rm= T)), labels = c("min","max"))+
		@@ -65,9 +69,11 @@ complex_featureplot<-function(
		axis.line = element_blank(),
		axis.text = element_blank(),
		axis.title=element_blank(),
		strip.background = element_blank(),
		strip.text = element_text(size=label.size),
		legend.title = element_text(size = 12),
		legend.position="left")+
		legend.title = element_blank(),
		legend.key.size = unit(0.5, 'cm'),
		legend.position="bottom")+
		facet_grid(group ~ gene)
		g <- change_strip_background(p, type = 'both', strip.color = strip.color)
		print(grid::grid.draw(g))
		}
		No newline at end of file

README.md

+2 −2

Original line number	Diff line number	Diff line
		@@ -111,8 +111,8 @@ The violin plot will look too messy in this scenario so it is not included in pl

		### 4. Umap geneplot across groups
		```
		png(filename = 'geneplot_umap.png', width = 4, height = 6,units = 'in', res = 100)
		complex_featureplot(iri.integrated, features = c("Havcr1","Slc34a1"), group = "Group", select = c("Control","12hours","6weeks"), order = T)
		png(filename = 'data/geneplot_umap.png', width = 8, height = 6,units = 'in', res = 100)
		complex_featureplot(iri.integrated, features = c("Havcr1", "Slc34a1", "Vcam1", "Krt20" , "Slc7a13"), group = "Group", select = c("Control","12hours","6weeks"), order = F)
		dev.off()
		```
		![alt text](https://github.com/HaojiaWu/Plot1cell/blob/master/data/geneplot_umap.png) <br />

data/geneplot_umap.png

+29.3 KiB (81.4 KiB)

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man/complex_featureplot.Rd

+9 −3

Original line number	Diff line number	Diff line
		@@ -10,12 +10,14 @@ complex_featureplot(
		group,
		select = NULL,
		cols = NULL,
		label.size = 14,
		order = F
		label.size = 12,
		order = F,
		strip.color = NULL,
		pt.size = 0.01
		)
		}
		\arguments{
		\item{seu_obj}{A complete Seurat object}
		\item{seu_obj}{A complete Seurat object.}

		\item{features}{Gene names to be plotted.}

		@@ -26,6 +28,10 @@ complex_featureplot(
		\item{cols}{Change the color legend.}

		\item{label.size}{Change the label size.}

		\item{strip.color}{Colors for the strip background.}

		\item{pt.size}{Point size for each cell.}
		}
		\value{
		A ggplot object

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