Violin plot of colData. — plotSCEViolinColData • singleCellTK

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

plotSCEViolinColData(
  inSCE,
  coldata,
  sample = NULL,
  groupBy = NULL,
  violin = TRUE,
  boxplot = TRUE,
  dots = TRUE,
  plotOrder = NULL,
  xlab = NULL,
  ylab = NULL,
  baseSize = 12,
  axisSize = NULL,
  axisLabelSize = NULL,
  dotSize = 0.1,
  transparency = 1,
  defaultTheme = TRUE,
  gridLine = FALSE,
  summary = NULL,
  summaryTextSize = 3,
  title = NULL,
  titleSize = NULL,
  hcutoff = NULL,
  hcolor = "red",
  hsize = 1,
  hlinetype = 1,
  vcutoff = NULL,
  vcolor = "red",
  vsize = 1,
  vlinetype = 1,
  combinePlot = "none",
  plotLabels = NULL
)

Arguments

inSCE: Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.
coldata: colData value that will be plotted.
sample: Character vector. Indicates which sample each cell belongs to.
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.
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.
plotOrder: Character vector. If set, reorders the violin plots in the order of the character vector when `groupBy` is set. Default NULL.
xlab: Character vector. Label for x-axis. Default NULL.
ylab: Character vector. Label for y-axis. Default NULL.
baseSize: The base font size for all text. Default 12. Can be overwritten by titleSize, axisSize, and axisLabelSize.
axisSize: Size of x/y-axis ticks. Default NULL.
axisLabelSize: Size of x/y-axis labels. Default NULL.
dotSize: Size of dots. Default 0.1.
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.
summaryTextSize: The text size of the summary statistic displayed above the violin plot. Default 3.
title: Title of plot. Default NULL.
titleSize: Size of title of plot. Default 15.
hcutoff: Adds a horizontal line with the y-intercept at given value. Default NULL.
hcolor: Character. A color available from `colors()`. Controls the color of the horizontal cutoff line, if drawn. Default 'black'.
hsize: Size of horizontal line, if drawn. Default 0.5.
hlinetype: Type of horizontal line, if drawn. can be specified with either an integer or a name (0 = blank, 1 = solid, 2 = dashed, 3 = dotted, 4 = dotdash, 5 = longdash, 6 = twodash). Default 1.
vcutoff: Adds a vertical line with the x-intercept at given value. Default NULL.
vcolor: Character. A color available from `colors()`. Controls the color of the vertical cutoff line, if drawn. Default 'black'.
vsize: Size of vertical line, if drawn. Default 0.5.
vlinetype: Type of vertical line, if drawn. can be specified with either an integer or a name (0 = blank, 1 = solid, 2 = dashed, 3 = dotted, 4 = dotdash, 5 = longdash, 6 = twodash). Default 1.
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 "none".
plotLabels: labels to each plot. If set to "default", will use the name of the samples as the labels. If set to "none", no label will be plotted.

Value

a ggplot of the violin plot of coldata.

Examples

data("mouseBrainSubsetSCE")
plotSCEViolinColData(
  inSCE = mouseBrainSubsetSCE,
  coldata = "age", groupBy = "sex"
)