plotEmptyDropsScatter: Plots for runEmptyDrops outputs.

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

Plots for runEmptyDrops outputs.

Description

A plotting function which visualizes outputs from the runEmptyDrops function stored in the colData slot of the SingleCellExperiment object via scatter plots.

Usage

plotEmptyDropsScatter(
  inSCE,
  sample = NULL,
  fdrCutoff = 0.01,
  defaultTheme = TRUE,
  dotSize = 0.1,
  title = NULL,
  titleSize = 18,
  xlab = NULL,
  ylab = NULL,
  axisSize = 12,
  axisLabelSize = 15,
  legendTitle = NULL,
  legendTitleSize = 12,
  legendSize = 10,
  combinePlot = "none",
  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.
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 0.1.
title	Title of plot. Default NULL.
titleSize	Size of title of plot. Default 18.
xlab	Character vector. Label for x-axis. Default NULL.
ylab	Character vector. Label for y-axis. Default NULL.
axisSize	Size of x/y-axis ticks. Default 12.
axisLabelSize	Size of x/y-axis labels. Default 15.
legendTitle	Title of legend. Default NULL.
legendTitleSize	size of legend title. Default 12.
legendSize	size of legend. Default 10.
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".
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

a ggplot object of the scatter plot.

See Also

runEmptyDrops, plotEmptyDropsResults

Examples

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

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