plotBubble: Plot Bubble plot

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Plot Bubble plot

Description

Plot a bubble plot with the color of the plot being the mean expression and the size of the dot being the percent of cells in the cluster expressing the gene.

Usage

plotBubble(
  inSCE,
  useAssay = "logcounts",
  featureNames,
  displayName = NULL,
  groupNames = "cluster",
  title = "",
  xlab = NULL,
  ylab = NULL,
  colorLow = "white",
  colorHigh = "blue",
  scale = FALSE
)

Arguments

inSCE	The single cell experiment to use.
useAssay	The assay to use.
featureNames	A string or vector of strings with each gene to aggregate.
displayName	A string that is the name of the column used for genes.
groupNames	The name of a colData entry that can be used as groupNames.
title	The title of the bubble plot
xlab	The x-axis label
ylab	The y-axis label
colorLow	The color to be used for lowest value of mean expression
colorHigh	The color to be used for highest value of mean expression
scale	Option to scale the data. Default: /codeFALSE. Selected assay will not be scaled.

Value

A ggplot of the bubble plot.

Examples

data("scExample")
plotBubble(inSCE=sce, useAssay="counts", featureNames=c("B2M", "MALAT1"),
displayName="feature_name", groupNames="type", title="cell type test",
xlab="gene", ylab="cluster", colorLow="white", colorHigh="blue")

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.