updates (5181250a) · Commits · github_fork / Plot1cell

R/plot_cell_fraction.R

+2 −2

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		@@ -6,9 +6,9 @@
		#' This function is to show the cell fraction changes across groups.
		#'
		#' @param seu_obj A complete Seurat object
		#' @param celltypes Cell types to be included in the dot plot. Default: all cell types.
		#' @param celltypes Cell types to be included in the plot. Default: all cell types.
		#' @param groupby The group to show on x axis. One of the column names in meta.data.
		#' @param show_replicate Whether or not to show the individual replicates from the graph. If TRUE, the replicate column names need to specify.
		#' @param show_replicate Whether or not to show the individual replicate on the graph. If TRUE, the replicate column name needs to specify in the argument rep_colname.
		#' @param rep_colname The column name for biological replicates in the meta data.
		#' @param strip.color Colors for the strip background
		#' @return A ggplot object

+4 −2

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		@@ -158,6 +158,7 @@ prepare_circlize_data <- function(
		#' @param do.label Whether to label the clusters
		#' @param contour.levels Which contour line to be drawn on the plot. Value: 0-1
		#' @param bg.color Canvas background color
		#' @param label.cex Label font size
		#' @param pt.size Point size of the graph
		#' @param kde2d.n Number of grid points in each direction. A kde2d parameter
		#' @param contour.nlevels Total number of levels in contour
		@@ -174,6 +175,7 @@ plot_circlize <- function(
		contour.nlevels = 100,
		bg.color='#F9F2E4',
		col.use=NULL,
		label.cex = 0.5,
		repel=FALSE
		) {
		data_plot %>%
		@@ -211,9 +213,9 @@ plot_circlize <- function(
		contour(z, drawlabels=F, nlevels= 100, levels = contour.levels,col = '#ae9c76', add=TRUE)
		if(do.label){
		if(repel){
		textplot(x=centers$x, y=centers$y, words = centers$Cluster,cex = 0.8, new = F,show.lines=F)
		textplot(x=centers$x, y=centers$y, words = centers$Cluster,cex = label.cex, new = F,show.lines=F)
		} else {
		text(centers$x,centers$y, labels=centers$Cluster, cex = 0.8, col = 'black')
		text(centers$x,centers$y, labels=centers$Cluster, cex = label.cex, col = 'black')
		}
		}
		}

+1 KiB (946 KiB)

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+3 −3

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		@@ -16,11 +16,11 @@ plot_cell_fraction(
		\arguments{
		\item{seu_obj}{A complete Seurat object}

		\item{celltypes}{Cell types to be included in the dot plot. Default: all cell types.}
		\item{celltypes}{Cell types to be included in the plot. Default: all cell types.}

		\item{groupby}{The group to show on x axis. One of the column names in meta.data.}

		\item{show_replicate}{Whether or not to show the individual replicates from the graph. If TRUE, the replicate column names need to specify.}
		\item{show_replicate}{Whether or not to show the individual replicate on the graph. If TRUE, the replicate column name needs to specify in the argument rep_colname.}

		\item{rep_colname}{The column name for biological replicates in the meta data.}

		@@ -30,5 +30,5 @@ plot_cell_fraction(
		A ggplot object
		}
		\description{
		This function to show the cell fraction changes across groups.
		This function is to show the cell fraction changes across groups.
		}

+3 −0

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		@@ -13,6 +13,7 @@ plot_circlize(
		contour.nlevels = 100,
		bg.color = "#F9F2E4",
		col.use = NULL,
		label.cex = 0.5,
		repel = FALSE
		)
		}
		@@ -33,6 +34,8 @@ plot_circlize(

		\item{col.use}{Colors used to label the cell type}

		\item{label.cex}{Label font size}

		\item{repel}{Whether or not to repel the cell type names on umap}
		}
		\value{