plotSCEDimReduceColData: Dimension reduction plot tool for colData

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

Dimension reduction plot tool for colData

Description

Plot results of reduced dimensions data and colors by annotation data stored in the colData slot.

Usage

plotSCEDimReduceColData(
  inSCE,
  colorBy,
  reducedDimName,
  sample = NULL,
  groupBy = NULL,
  conditionClass = NULL,
  shape = NULL,
  xlab = NULL,
  ylab = NULL,
  baseSize = 12,
  axisSize = NULL,
  axisLabelSize = NULL,
  dim1 = NULL,
  dim2 = NULL,
  bin = NULL,
  binLabel = NULL,
  dotSize = 0.1,
  transparency = 1,
  colorScale = NULL,
  colorLow = "white",
  colorMid = "gray",
  colorHigh = "blue",
  defaultTheme = TRUE,
  title = NULL,
  titleSize = 15,
  labelClusters = TRUE,
  clusterLabelSize = 3.5,
  legendTitle = NULL,
  legendTitleSize = NULL,
  legendSize = NULL,
  combinePlot = "none",
  plotLabels = NULL
)

Arguments

inSCE	Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.
colorBy	Color by a condition(any column of the annotation data). Required.
reducedDimName	Saved dimension reduction matrix name in the SingleCellExperiment object. Required.
sample	Character vector. Indicates which sample each cell belongs to.
groupBy	Group by a condition(any column of the annotation data). Default NULL.
conditionClass	Class of the annotation data used in colorBy. Options are NULL, "factor" or "numeric". If NULL, class will default to the original class. Default NULL.
shape	Add shapes to each condition.
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, legendSize, legendTitleSize.
axisSize	Size of x/y-axis ticks. Default NULL.
axisLabelSize	Size of x/y-axis labels. Default NULL.
dim1	1st dimension to be used for plotting. Can either be a string which specifies the name of the dimension to be plotted from reducedDims, or a numeric value which specifies the index of the dimension to be plotted. Default is NULL.
dim2	2nd dimension to be used for plotting. Can either be a string which specifies the name of the dimension to be plotted from reducedDims, or a numeric value which specifies the index of the dimension to be plotted. Default is NULL.
bin	Numeric vector. If single value, will divide the numeric values into the 'bin' groups. If more than one value, will bin numeric values using values as a cut point.
binLabel	Character vector. Labels for the bins created by the 'bin' parameter. Default NULL.
dotSize	Size of dots. Default 0.1.
transparency	Transparency of the dots, values will be 0-1. Default 1.
colorScale	Vector. Needs to be same length as the number of unique levels of colorBy. Will be used only if conditionClass = "factor" or "character". Default NULL.
colorLow	Character. A color available from 'colors()'. The color will be used to signify the lowest values on the scale. Default 'white'.
colorMid	Character. A color available from 'colors()'. The color will be used to signify the midpoint on the scale. Default 'gray'.
colorHigh	Character. A color available from 'colors()'. The color will be used to signify the highest values on the scale. Default 'blue'.
defaultTheme	adds grid to plot when TRUE. Default TRUE.
title	Title of plot. Default NULL.
titleSize	Size of title of plot. Default 15.
labelClusters	Logical. Whether the cluster labels are plotted.
clusterLabelSize	Numeric. Determines the size of cluster label when 'labelClusters' is set to TRUE. Default 3.5.
legendTitle	title of legend. Default NULL.
legendTitleSize	size of legend title. Default 12.
legendSize	size of legend. Default NULL. Default FALSE.
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 reduced dimension plot of coldata.

Examples

data("mouseBrainSubsetSCE")
plotSCEDimReduceColData(
  inSCE = mouseBrainSubsetSCE, colorBy = "tissue",
  shape = NULL, conditionClass = "factor",
  reducedDimName = "TSNE_counts",
  xlab = "tSNE1", ylab = "tSNE2", labelClusters = TRUE
)

plotSCEDimReduceColData(
  inSCE = mouseBrainSubsetSCE, colorBy = "age",
  shape = NULL, conditionClass = "numeric",
  reducedDimName = "TSNE_counts", bin = c(-Inf, 20, 25, +Inf),
  xlab = "tSNE1", ylab = "tSNE2", labelClusters = FALSE
)

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