update plot functions (d0b5ce18) · Commits · github_fork / DAseq2

NAMESPACE

+1 −0

Original line number	Diff line number	Diff line
		@@ -16,6 +16,7 @@ import(RANN)
		import(Seurat)
		import(cowplot)
		import(ggplot2)
		import(ggrepel)
		import(glmnet)
		import(reticulate)
		import(scales)

R/plots.R

+31 −14

Original line number	Diff line number	Diff line
		#' @import ggplot2
		#' @import cowplot
		#' @import ggrepel
		NULL


		@@ -16,14 +17,13 @@ NULL
		#' @return a ggplot object
		#' @export
		#'
		plotCellScore <- function(X, score, cell.col = c("blue","white","red"), size = 0.5, alpha = 1){
		plotCellScore <- function(X, score, cell.col = c("blue","white","red"), size = 0.5, alpha = 1, shape = 16){
		# Add colnames for X
		colnames(X) <- c("Dim1","Dim2")

		# Plot cells with labels
		myggplot <- ggplot() + theme_cowplot() +
		geom_point(data = data.frame(Dim1 = X[,1], Dim2 = X[,2], Score = score),
		aes(x = Dim1, y = Dim2, col = Score), size = size, alpha = alpha) +
		myggplot <- ggplot(data = data.frame(Dim1 = X[,1], Dim2 = X[,2], Score = score)) + theme_cowplot() +
		geom_point(aes(x = Dim1, y = Dim2, col = Score), shape = shape, size = size, alpha = alpha) +
		scale_color_gradientn(colours = cell.col)

		return(myggplot)
		@@ -49,11 +49,11 @@ plotDAsite <- function(X, site.list, size = 0.5, cols = NULL){
		}

		myggplot <- ggplot() + theme_cowplot() +
		geom_point(data = data.frame(X), aes(Dim1, Dim2), col = "gray", size = size) +
		geom_point(data = data.frame(X), aes(Dim1, Dim2), shape = 16, col = "gray", size = size) +
		geom_point(
		data = data.frame(X[unlist(site.list),]),
		aes(Dim1, Dim2, col = as.factor(site.label[unlist(site.list)])),
		size = size
		shape = 16, size = size
		) + theme(legend.position = "none")

		if(!is.null(cols) & length(cols) == length(site.list)){
		@@ -77,19 +77,24 @@ plotDAsite <- function(X, site.list, size = 0.5, cols = NULL){
		#' @param alpha numeric between 0 to 1, dot opacity for each cell, default 1
		#' @param do.label a logical value indicating whether to add text to mark each cell label
		#' @param label.size numeric, size of text labels, default 4
		#' @param label.repel a logical value indicating whether to repel the labels to avoid overlapping, default False
		#' @param label.plot cell labels to add text annotations, default NULL, add text for all labels
		#'
		#' @return a ggplot object
		#' @export
		#'
		plotCellLabel <- function(X, label, cell.col = NULL, size = 0.5, alpha = 1, do.label = T, label.size = 4){
		plotCellLabel <- function(
		X, label, cell.col = NULL, size = 0.5, alpha = 1, shape = 16,
		do.label = T, label.size = 4, label.repel = F, label.plot = NULL
		){
		# Add colnames for X
		colnames(X) <- c("Dim1","Dim2")

		# Plot cells with labels
		myggplot <- ggplot() + theme_cowplot() +
		geom_point(data = data.frame(Dim1 = X[,1], Dim2 = X[,2], Group = label, stringsAsFactors = F),
		aes(x = Dim1, y = Dim2, col = Group), size = size, alpha = alpha) +
		guides(colour = guide_legend(override.aes = list(size=3,alpha=1), title = NULL))
		myggplot <- ggplot(data = data.frame(Dim1 = X[,1], Dim2 = X[,2], Group = label, stringsAsFactors = F)) +
		theme_cowplot() +
		geom_point(aes(x = Dim1, y = Dim2, col = Group), shape = shape, size = size, alpha = alpha) +
		guides(colour = guide_legend(override.aes = list(size=3,alpha=1,shape=19), title = NULL))

		# Change cell color
		if(!is.null(cell.col)){
		@@ -98,12 +103,24 @@ plotCellLabel <- function(X, label, cell.col = NULL, size = 0.5, alpha = 1, do.l

		# Label text
		if(do.label){
		if(is.null(label.plot)){
		mylabels <- unique(label)
		} else {
		mylabels <- label.plot
		}
		labeldim1 <- by(X[,1], INDICES = label, FUN = median)[mylabels]
		labeldim2 <- by(X[,2], INDICES = label, FUN = median)[mylabels]

		if(!label.repel){
		myggplot <- myggplot +
		annotate("text", x = labeldim1, y = labeldim2, label = as.character(mylabels), size = label.size)
		} else {
		myggplot <- myggplot +
		geom_text_repel(
		data = data.frame(x = labeldim1, y = labeldim2, text = mylabels), aes(x,y, label = text),
		segment.colour = NA, size = label.size
		)
		}
		}

		return(myggplot)

man/plotCellLabel.Rd

+6 −1

Original line number	Diff line number	Diff line
		@@ -5,7 +5,8 @@
		\title{Plot cell labels}
		\usage{
		plotCellLabel(X, label, cell.col = NULL, size = 0.5, alpha = 1,
		do.label = T, label.size = 4)
		shape = 16, do.label = T, label.size = 4, label.repel = F,
		label.plot = NULL)
		}
		\arguments{
		\item{X}{matrix, 2D embedding of each cell for the plot}
		@@ -21,6 +22,10 @@ plotCellLabel(X, label, cell.col = NULL, size = 0.5, alpha = 1,
		\item{do.label}{a logical value indicating whether to add text to mark each cell label}

		\item{label.size}{numeric, size of text labels, default 4}

		\item{label.repel}{a logical value indicating whether to repel the labels to avoid overlapping, default False}

		\item{label.plot}{cell labels to add text annotations, default NULL, add text for all labels}
		}
		\value{
		a ggplot object

man/plotCellScore.Rd

+1 −1

Original line number	Diff line number	Diff line
		@@ -5,7 +5,7 @@
		\title{Plot a score for each cell}
		\usage{
		plotCellScore(X, score, cell.col = c("blue", "white", "red"),
		size = 0.5, alpha = 1)
		size = 0.5, alpha = 1, shape = 16)
		}
		\arguments{
		\item{X}{matrix, 2D embedding of each cell for the plot}

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