plotDecontXResults: Plots for runDecontX outputs.

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

Plots for runDecontX outputs.

Description

A wrapper function which visualizes outputs from the runDecontX function stored in the colData slot of the SingleCellExperiment object via various plots.

Usage

plotDecontXResults(
  inSCE,
  sample = NULL,
  bgResult = FALSE,
  shape = NULL,
  groupBy = NULL,
  combinePlot = "all",
  violin = TRUE,
  boxplot = FALSE,
  dots = TRUE,
  reducedDimName = "UMAP",
  xlab = NULL,
  ylab = NULL,
  dim1 = NULL,
  dim2 = NULL,
  bin = NULL,
  binLabel = NULL,
  defaultTheme = TRUE,
  dotSize = 0.5,
  summary = "median",
  summaryTextSize = 3,
  transparency = 1,
  baseSize = 15,
  titleSize = NULL,
  axisLabelSize = NULL,
  axisSize = NULL,
  legendSize = NULL,
  legendTitleSize = NULL,
  relHeights = 1,
  relWidths = c(1, 1, 1),
  plotNCols = NULL,
  plotNRows = NULL,
  labelSamples = TRUE,
  labelClusters = TRUE,
  clusterLabelSize = 3.5,
  samplePerColumn = TRUE,
  sampleRelHeights = 1,
  sampleRelWidths = 1
)

Arguments

inSCE	Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runDecontX. Required.
sample	Character vector. Indicates which sample each cell belongs to. Default NULL.
bgResult	Boolean. If TRUE, will plot decontX results generated with raw/droplet matrix Default FALSE.
shape	If provided, add shapes based on the value.
groupBy	Groupings for each numeric value. A user may input a vector equal length to the number of the samples in the SingleCellExperiment object, or can be retrieved from the colData slot. Default NULL.
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".
violin	Boolean. If TRUE, will plot the violin plot. Default TRUE.
boxplot	Boolean. If TRUE, will plot boxplots for each violin plot. Default TRUE.
dots	Boolean. If TRUE, will plot dots for each violin plot. Default TRUE.
reducedDimName	Saved dimension reduction name in the SingleCellExperiment object. Required. Default = "UMAP"
xlab	Character vector. Label for x-axis. Default NULL.
ylab	Character vector. Label for y-axis. Default NULL.
dim1	1st dimension to be used for plotting. Can either be a string which specifies the name of the dimension to be plotted from reducedDims, or a numeric value which specifies the index of the dimension to be plotted. Default is NULL.
dim2	2nd dimension to be used for plotting. Can either be a string which specifies the name of the dimension to be plotted from reducedDims, or a numeric value which specifies the index of the dimension to be plotted. Default is NULL.
bin	Numeric vector. If single value, will divide the numeric values into the 'bin' groups. If more than one value, will bin numeric values using values as a cut point.
binLabel	Character vector. Labels for the bins created by the 'bin' parameter. Default NULL.
defaultTheme	Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.
dotSize	Size of dots. Default 0.5.
summary	Adds a summary statistic, as well as a crossbar to the violin plot. Options are "mean" or "median". Default NULL.
summaryTextSize	The text size of the summary statistic displayed above the violin plot. Default 3.
transparency	Transparency of the dots, values will be 0-1. Default 1.
baseSize	The base font size for all text. Default 12. Can be overwritten by titleSize, axisSize, and axisLabelSize, legendSize, legendTitleSize.
titleSize	Size of title of plot. Default NULL.
axisLabelSize	Size of x/y-axis labels. Default NULL.
axisSize	Size of x/y-axis ticks. Default NULL.
legendSize	size of legend. Default NULL.
legendTitleSize	size of legend title. Default NULL.
relHeights	Relative heights of plots when combine is set.
relWidths	Relative widths of plots when combine is set.
plotNCols	Number of columns when plots are combined in a grid.
plotNRows	Number of rows when plots are combined in a grid.
labelSamples	Will label sample name in title of plot if TRUE. Default TRUE.
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.
samplePerColumn	If TRUE, when there are multiple samples and combining by "all", the output .ggplot will have plots from each sample on a single column. Default TRUE.
sampleRelHeights	If there are multiple samples and combining by "all", the relative heights for each plot.
sampleRelWidths	If there are multiple samples and combining by "all", the relative widths for each plot.

Value

list of .ggplot objects

Examples

data(scExample, package="singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- runDecontX(sce)
plotDecontXResults(inSCE=sce, reducedDimName="decontX_UMAP")

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