plotSCEScatter: Dimension reduction plot tool for all types of data

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

Dimension reduction plot tool for all types of data

Description

Plot results of reduced dimensions data of counts stored in any slot in the SingleCellExperiment object.

Usage

plotSCEScatter(
  inSCE,
  annotation,
  reducedDimName = NULL,
  slot = NULL,
  sample = NULL,
  feature = NULL,
  groupBy = NULL,
  shape = NULL,
  conditionClass = NULL,
  xlab = NULL,
  ylab = NULL,
  axisSize = 10,
  axisLabelSize = 10,
  dim1 = NULL,
  dim2 = NULL,
  bin = NULL,
  binLabel = NULL,
  dotSize = 0.1,
  transparency = 1,
  colorLow = "white",
  colorMid = "gray",
  colorHigh = "blue",
  defaultTheme = TRUE,
  title = NULL,
  titleSize = 15,
  labelClusters = TRUE,
  legendTitle = NULL,
  legendTitleSize = 12,
  legendSize = 10,
  combinePlot = "none",
  plotLabels = NULL
)

Arguments

inSCE	Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.
annotation	Desired vector within the slot used for plotting. Default NULL.
reducedDimName	saved dimension reduction name in the SingleCellExperiment object.
slot	Desired slot of SingleCellExperiment used for plotting. Possible options: "assays", "colData", "metadata", "reducedDims". Default NULL.
sample	Character vector. Indicates which sample each cell belongs to.
feature	name of feature stored in assay of SingleCellExperiment object. Will be used only if "assays" slot is chosen. Default NULL.
groupBy	Group by a condition(any column of the annotation data). Default NULL.
shape	add shapes to each condition.
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.
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.
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.
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.
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 "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 dimensions.

Examples

data("mouseBrainSubsetSCE")
plotSCEScatter(
  inSCE = mouseBrainSubsetSCE, legendTitle = NULL,
  slot = "assays", annotation = "counts", feature = "Apoe",
  reducedDimName = "TSNE_counts", labelClusters = FALSE
)

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