Plot SoupX Result

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.

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.

Examples

if (FALSE) {
sce <- importExampleData("pbmc3k")
sce <- runSoupX(sce, sample = "sample")
plotSoupXResults(sce, sample = "sample")
}

Arguments

Value

See also

Examples