plotSoupXResults: Plot SoupX Result

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

Plot SoupX Result

Description

This function will generate a combination of plots basing on the correction done by SoupX. For each sample, there will be a UMAP with cluster labeling, followed by a number of UMAPs showing the change in selected top markers. The cluster labeling is what should be used for SoupX to estimate the contamination. The Soup Fraction is calculated by subtracting the gene expression value of the output corrected matrix from that of the original input matrix, and then devided by the input.

Usage

plotSoupXResults(
  inSCE,
  sample = NULL,
  background = FALSE,
  reducedDimName = NULL,
  plotNCols = 3,
  plotNRows = 2,
  baseSize = 8,
  combinePlot = c("all", "sample", "none"),
  xlab = NULL,
  ylab = NULL,
  dim1 = NULL,
  dim2 = NULL,
  labelClusters = FALSE,
  clusterLabelSize = 3.5,
  defaultTheme = TRUE,
  dotSize = 0.5,
  transparency = 1,
  titleSize = NULL,
  axisLabelSize = NULL,
  axisSize = NULL,
  legendSize = NULL,
  legendTitleSize = NULL
)

Arguments

inSCE	A SingleCellExperiment object. With runSoupX already applied.
sample	Character vector. Indicates which sample each cell belongs to. Default NULL.
background	Logical. Whether background was applied when running runSoupX. Default FALSE.
reducedDimName	Character. The embedding to use for plotting. Leave it NULL for using the sample-specific UMAPs generated when running runSoupX. Default NULL.
plotNCols	Integer. Number of columns for the plot grid per sample. Will determine the number of top markers to show together with plotNRows. Default 3.
plotNRows	Integer. Number of rows for the plot grid per sample. Will determine the number of top markers to show together with plotNCols. Default 2.
baseSize	Numeric. The base font size for all text. Default 12. Can be overwritten by titleSize, axisSize, and axisLabelSize, legendSize, legendTitleSize. Default 8.
combinePlot	Must be either "all", "sample", or "none". "all" will combine all plots into a single .ggplot object, while "sample" will output a list of plots separated by sample. Default "all".
xlab	Character vector. Label for x-axis. Default NULL.
ylab	Character vector. Label for y-axis. Default NULL.
dim1	See plotSCEDimReduceColData. Default NULL.
dim2	See plotSCEDimReduceColData. Default NULL.
labelClusters	Logical. Whether the cluster labels are plotted. Default FALSE.
clusterLabelSize	Numeric. Determines the size of cluster label when labelClusters is set to TRUE. Default 3.5.
defaultTheme	Logical. Adds grid to plot when TRUE. Default TRUE.
dotSize	Numeric. Size of dots. Default 0.5.
transparency	Numeric. Transparency of the dots, values will be from 0 to 1. Default 1.
titleSize	Numeric. Size of title of plot. Default 15.
axisLabelSize	Numeric. Size of x/y-axis labels. Default NULL.
axisSize	Numeric. Size of x/y-axis ticks. Default NULL.
legendSize	Numeric. Size of legend. Default NULL.
legendTitleSize	Numeric. Size of legend title. Default NULL.

Value

ggplot object of the combination of UMAPs. See description.

See Also

runSoupX

Examples

## Not run: 
sce <- importExampleData("pbmc3k")
sce <- runSoupX(sce, sample = "sample")
plotSoupXResults(sce, sample = "sample")

## End(Not run)

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