Bud fixes (7bcfb8e5) · Commits · github_fork / Plot1cell

R/plot_dot.R

+10 −4

Original line number	Diff line number	Diff line
		@@ -15,6 +15,7 @@
		#' @param splitby The group to separate the gene expression. One of the column names in meta.data.
		#' @param scale.by Methods to scale the dot size. "radius" or "size"
		#' @param strip.color Colors for the strip background
		#' @param do.scale Whether or not to scale the dot when percentage expression of the gene is less than 20.
		#' @return A ggplot object
		#' @export
		complex_dotplot_single <- function(
		@@ -23,6 +24,7 @@ complex_dotplot_single <- function(
		groupby,
		splitby=NULL,
		strip.color=NULL,
		do.scale=T,
		scale.by='radius'
		){
		if (is.null(levels(seu_obj@meta.data[,groupby]))){
		@@ -79,7 +81,7 @@ complex_dotplot_single <- function(
		geom_tile(fill="white", color="white") +
		geom_point(aes( colour=avg.exp, size =pct.exp)) +
		scale_color_gradientn(colours = colorRampPalette(c('grey80','lemonchiffon1','indianred1','darkred'))(255))+
		theme(axis.line = element_blank(),
		theme(panel.background = element_rect(fill = "white", colour = "black"),
		axis.text.x = element_text(angle = 45, hjust = 1),
		plot.title = element_text(size = 16,hjust = 0.5, face = 'bold'),
		axis.text = element_text(size = 12),
		@@ -88,11 +90,15 @@ complex_dotplot_single <- function(
		legend.title = element_text(size = 12),
		legend.position="right")+
		ylab("")+xlab("")+ggtitle(feature)
		if(do.scale){
		p = p + scale_size(range = c(0, 10))
		} else {
		if(max(data_plot$pct.exp)>=20){
		p = p + scale_size(range = c(0, 10))
		} else {
		p = p + scale.func(range = c(0, 10), limits = c(0, 20))
		}
		}
		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)
		@@ -145,7 +151,7 @@ complex_dotplot_multiple <- function(
		geom_point(aes( colour=avg.exp, size =pct.exp), alpha=0.9) +
		scale_color_gradientn(colours = grDevices::colorRampPalette(c('grey80','lemonchiffon1','indianred1','darkred'))(255))+
		scale_size(range = c(0, 10))+
		theme( axis.line = element_blank(),
		theme(panel.background = element_rect(fill = "white", colour = "black"),
		axis.text.x = element_text(angle = 45, hjust = 1),
		plot.title = element_text(size = 16,hjust = 0.5, face = 'bold'),
		axis.text = element_text(size = 12),

man/complex_dotplot_single.Rd

+3 −0

Original line number	Diff line number	Diff line
		@@ -10,6 +10,7 @@ complex_dotplot_single(
		groupby,
		splitby = NULL,
		strip.color = NULL,
		do.scale = T,
		scale.by = "radius"
		)
		}
		@@ -24,6 +25,8 @@ complex_dotplot_single(

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

		\item{do.scale}{Whether or not to scale the dot when percentage expression of the gene is less than 20.}

		\item{scale.by}{Methods to scale the dot size. "radius" or "size"}
		}
		\value{

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