plotSCEViolin: Violin plot of any data stored in the SingleCellExperiment...

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

Violin plot of any data stored in the SingleCellExperiment object.

Description

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

Usage

plotSCEViolin(
  inSCE,
  slotName,
  itemName,
  feature = NULL,
  sample = NULL,
  dimension = NULL,
  groupBy = NULL,
  violin = TRUE,
  boxplot = TRUE,
  dots = TRUE,
  plotOrder = NULL,
  xlab = NULL,
  ylab = NULL,
  axisSize = 10,
  axisLabelSize = 10,
  dotSize = 0.1,
  transparency = 1,
  defaultTheme = TRUE,
  gridLine = FALSE,
  summary = NULL,
  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.
slotName	Desired slot of SingleCellExperiment used for plotting. Possible options: "assays", "colData", "metadata", "reducedDims". Required.
itemName	Desired vector within the slot used for plotting. Required.
feature	Desired name of feature stored in assay of SingleCellExperiment object. Only used when "assays" slotName is selected. Default NULL.
sample	Character vector. Indicates which sample each cell belongs to.
dimension	Desired dimension stored in the specified reducedDims. Either an integer which indicates the column or a character vector specifies column name. By default, the 1st dimension/column will be used. Only used when "reducedDims" slotName is selected. Default NULL.
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.
axisSize	Size of x/y-axis ticks. Default 10.
axisLabelSize	Size of x/y-axis labels. Default 10.
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.
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.

Examples

data("mouseBrainSubsetSCE")
plotSCEViolin(
  inSCE = mouseBrainSubsetSCE, slotName = "assays",
  itemName = "counts", feature = "Apoe", groupBy = "sex"
)

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