plotSCEBarColData: Bar plot of colData.

Description Usage Arguments Value Examples

View source: R/ggPlotting.R

Description

Visualizes values stored in the colData slot of a SingleCellExperiment object via a bar plot.

Usage

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plotSCEBarColData(
  inSCE,
  sample = NULL,
  coldata,
  groupBy = NULL,
  dots = TRUE,
  xlab = NULL,
  ylab = NULL,
  axisSize = 10,
  axisLabelSize = 10,
  dotSize = 1,
  transparency = 1,
  defaultTheme = TRUE,
  gridLine = FALSE,
  summary = NULL,
  title = NULL,
  titleSize = NULL,
  combinePlot = TRUE
)

Arguments

inSCE

Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.

sample

Character vector. Indicates which sample each cell belongs to.

coldata

colData value that will be plotted.

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.

dots

Boolean. If TRUE, will plot dots for each violin plot. Default TRUE.

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 10.

axisLabelSize

Size of x/y-axis labels. Default 10.

dotSize

Size of dots. Default 1.

transparency

Transparency of the dots, values will be 0-1. Default 1.

defaultTheme

Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.

gridLine

Adds a horizontal grid line if TRUE. Will still be drawn even if defaultTheme is TRUE. Default FALSE.

summary

Adds a summary statistic, as well as a crossbar to the violin plot. Options are "mean" or "median". Default NULL.

title

Title of plot. Default NULL.

titleSize

Size of title of plot. Default 15.

combinePlot

Boolean. If multiple plots are generated (multiple samples, etc.), will combined plots using 'cowplot::plot_grid'. Default TRUE.

Value

a ggplot of the barplot of coldata.

Examples

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plotSCEBarColData(
  inSCE = mouseBrainSubsetSCE,
  coldata = "age", groupBy = "sex"
)

singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.