plotEmptyDropsResults: Plots for runEmptyDrops outputs.

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

Plots for runEmptyDrops outputs.

Description

A wrapper function which visualizes outputs from the runEmptyDrops function stored in the colData slot of the SingleCellExperiment object.

Usage

plotEmptyDropsResults(
  inSCE,
  sample = NULL,
  combinePlot = "all",
  fdrCutoff = 0.01,
  defaultTheme = TRUE,
  dotSize = 0.5,
  titleSize = 18,
  axisLabelSize = 18,
  axisSize = 15,
  legendSize = 15,
  legendTitleSize = 16,
  relHeights = 1,
  relWidths = 1,
  samplePerColumn = TRUE,
  sampleRelHeights = 1,
  sampleRelWidths = 1
)

Arguments

inSCE	Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runEmptyDrops. Required.
sample	Character vector or colData variable name. Indicates which sample each cell belongs to. Default NULL.
combinePlot	Must be either "all", "sample", or object, "none". "all" will combine all plots into a single .ggplot while "sample" will output a list of plots separated by sample. Default "all".
fdrCutoff	Numeric. Thresholds barcodes based on the FDR values from runEmptyDrops as "Empty Droplet" or "Putative Cell". Default 0.01.
defaultTheme	Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.
dotSize	Size of dots. Default 0.5.
titleSize	Size of title of plot. Default 18.
axisLabelSize	Size of x/y-axis labels. Default 18.
axisSize	Size of x/y-axis ticks. Default 15.
legendSize	size of legend. Default 15.
legendTitleSize	size of legend title. Default 16.
relHeights	Relative heights of plots when combine is set. Default 1.
relWidths	Relative widths of plots when combine is set. Default 1.
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. Default 1.
sampleRelWidths	If there are multiple samples and combining by "all", the relative widths for each plot. Default 1.

Value

list of .ggplot objects

See Also

runEmptyDrops, plotEmptyDropsScatter

Examples

data(scExample, package = "singleCellTK")
sce <- runEmptyDrops(inSCE = sce)
plotEmptyDropsResults(inSCE = sce)

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