plotSCEDimReduceFeatures: Dimension reduction plot tool for assay data

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

Dimension reduction plot tool for assay data

Description

Plot results of reduced dimensions data and colors by feature data stored in the assays slot.

Usage

plotSCEDimReduceFeatures(
  inSCE,
  feature,
  reducedDimName,
  sample = NULL,
  featureLocation = NULL,
  featureDisplay = NULL,
  shape = NULL,
  useAssay = "logcounts",
  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,
  legendTitle = NULL,
  legendSize = 10,
  legendTitleSize = 12,
  groupBy = NULL,
  combinePlot = "none",
  plotLabels = NULL
)

Arguments

inSCE	Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.
feature	Name of feature stored in assay of SingleCellExperiment object.
reducedDimName	saved dimension reduction name in the SingleCellExperiment object. Required.
sample	Character vector. Indicates which sample each cell belongs to.
featureLocation	Indicates which column name of rowData to query gene.
featureDisplay	Indicates which column name of rowData to use to display feature for visualization.
shape	add shapes to each condition. Default NULL.
useAssay	Indicate which assay to use. The default is "logcounts"
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.
legendTitle	title of legend. Default NULL.
legendSize	size of legend. Default 10.
legendTitleSize	size of legend title. Default 12.
groupBy	Facet wrap the scatterplot based on value. Default NULL.
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 feature data.

Examples

data("mouseBrainSubsetSCE")
plotSCEDimReduceFeatures(
  inSCE = mouseBrainSubsetSCE, feature = "Apoe",
  shape = NULL, reducedDimName = "TSNE_counts",
  useAssay = "counts", xlab = "tSNE1", ylab = "tSNE2"
)

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