fix colors (d9a5bb7b) · Commits · github_fork / Plot1cell

R/plot_cell_fraction.R

+1 −1

Original line number	Diff line number	Diff line
		@@ -70,7 +70,7 @@ plot_cell_fraction<-function(

		if(show_replicate){
		p <- p + geom_quasirandom(size=1,width = 0.2, color='midnightblue', alpha=0.8, groupOnX = F)+facet_wrap(~celltype, scales = 'free_y', ncol = length(celltypes))
		g <- change_strip_background(p, type = 'top', n.color = length(celltypes), strip.color = strip.color)
		g <- change_strip_background(p, type = 'top', strip.color = strip.color)
		print(grid.draw(g))
		} else {
		p

R/plot_dot.R

+2 −2

Original line number	Diff line number	Diff line
		@@ -108,7 +108,7 @@ complex_dotplot_single <- function(
		}
		if(!is.null(splitby)){
		p <- p +facet_wrap(~splitby, scales = 'free_x')
		g <- change_strip_background(p, type = 'top', n.color = length(levels(seu_obj)), strip.color = strip.color)
		g <- change_strip_background(p, type = 'top', strip.color = strip.color)
		print(grid.draw(g))
		} else {
		p
		@@ -172,7 +172,7 @@ complex_dotplot_multiple <- function(
		ylab("")+xlab("")+ggtitle('')+
		facet_wrap(~celltype, ncol = length(levels(seu_obj)))
		)
		g <- change_strip_background(p, type = 'top', n.color = length(levels(seu_obj)), strip.color = strip.color)
		g <- change_strip_background(p, type = 'top', strip.color = strip.color)
		print(grid.draw(g))
		}

R/plot_violin.R

+6 −25

Original line number	Diff line number	Diff line
		@@ -15,6 +15,7 @@
		#' @param font.size Font size for the labels.
		#' @param pt.size Point size for the data points on the violin
		#' @param splitby Group to split the gene expression. Only works when length(groups)==1.
		#' @param strip.color Colors for the strip background
		#' @return A ggplot object
		#' @export

		@@ -26,7 +27,8 @@ complex_vlnplot_single <- function(
		add.dot = T,
		font.size=14,
		pt.size=0.1,
		splitby=NULL
		splitby=NULL,
		strip.color=NULL
		){
		if(length(feature)>1){
		stop("Only one gene is allowed in this method. Please use complex_vlnplot_multiple if you want to plot multiple genes.")
		@@ -67,18 +69,7 @@ complex_vlnplot_single <- function(
		}
		if(!is.null(splitby)){
		p = p + facet_wrap(as.formula(paste("~", splitby)), scales = 'free_x')
		g <- ggplot_gtable(ggplot_build(p))
		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(celltypes) + length(names(table(gene_count[,splitby])))
		fills <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(12, "Set3"))(ncol)
		k <- 1
		for (i in strip_both) {
		j <- which(grepl('rect', g$grobs[[i]]$grobs[[1]]$childrenOrder))
		g$grobs[[i]]$grobs[[1]]$children[[j]]$gp$fill <- fills[k]
		k <- k+1
		}
		g <- change_strip_background(p, type = 'top', strip.color = strip.color)
		print(grid::grid.draw(g))
		} else {
		p
		@@ -108,6 +99,7 @@ complex_vlnplot_single <- function(
		p<- patchwork::wrap_plots(plotlist = plot_list, ncol = 1) + patchwork::plot_annotation(title = feature) & theme(plot.title = element_text(hjust = 0.5, size = (font.size +2)))
		p
		} else {
		gene_count$celltype<-factor(gene_count$celltype, levels = celltypes)
		p<-ggplot(gene_count, aes_string(x = groups, y = feature, fill = groups)) +
		facet_grid(as.formula(paste("celltype","~", splitby)), scales = "free_x") +
		geom_violin(scale = 'width', adjust = 1, trim = TRUE, size=0.3, alpha=0.5, color="pink")+
		@@ -123,18 +115,7 @@ complex_vlnplot_single <- function(
		if(add.dot){
		p = p + geom_quasirandom(size=pt.size, alpha=0.2)
		}
		g <- ggplot_gtable(ggplot_build(p))
		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(celltypes) + length(names(table(gene_count[,splitby])))
		fills <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(12, "Set3"))(ncol)
		k <- 1
		for (i in strip_both) {
		j <- which(grepl('rect', g$grobs[[i]]$grobs[[1]]$childrenOrder))
		g$grobs[[i]]$grobs[[1]]$children[[j]]$gp$fill <- fills[k]
		k <- k+1
		}
		g <- change_strip_background(p, type = 'both', strip.color = strip.color)
		print(grid::grid.draw(g))
		}
		}

R/utils.R

+9 −6

Original line number	Diff line number	Diff line
		@@ -385,27 +385,30 @@ firstup <- function(

		#' A function to change the strip background color in ggplot
		#' @param ggplt_obj A ggplot object
		#' @param n.color Number of colors.
		#' @param type Strip on the "top" side only or "both" sides
		#' @param strip.color A color vector
		#' @export
		#'
		change_strip_background <- function(
		ggplt_obj,
		type = "top",
		n.color,
		strip.color=NULL
		){
		g <- ggplot_gtable(ggplot_build(ggplt_obj))
		if(type == "top"){
		strip_both <- which(grepl('strip-t', g$layout$name))
		fills<-strip.color
		if(is.null(fills)){
		fills<- scales::hue_pal(l=90)(length(strip_both))
		}
		} else {
		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)
		}
		fills<-strip.color
		if(is.null(strip.color)){
		fills<- scales::hue_pal()(n.color)
		if(is.null(fills)){
		fills<- c(scales::hue_pal(l=90)(length(strip_t)),scales::hue_pal(l=90)(length(strip_r)))
		}
		}
		k <- 1
		for (i in strip_both) {

data/cell_fraction.png

+592 B (170 KiB)

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