plotDimRed: Plot dimensionality reduction from computed metrics including...

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

Plot dimensionality reduction from computed metrics including PCA, ICA, tSNE and UMAP

Description

Plot dimensionality reduction from computed metrics including PCA, ICA, tSNE and UMAP

Usage

plotDimRed(
  inSCE,
  useReduction,
  showLegend = FALSE,
  xDim = 1,
  yDim = 2,
  xAxisLabel = NULL,
  yAxisLabel = NULL
)

Arguments

inSCE	Input SCE object
useReduction	Reduction to plot
showLegend	If legends should be plotted or not
xDim	Numeric value indicating the dimension to use for X-axis. Default is 1 (refers to PC1).
yDim	Numeric value indicating the dimension to use for Y-axis. Default is 2 (refers to PC2).
xAxisLabel	Specify the label for x-axis. Default is NULL which will specify the label as 'x'.
yAxisLabel	Specify the label for y-axis. Default is NULL which will specify the label as 'y'.

Value

plot object

Examples

data("mouseBrainSubsetSCE", package = "singleCellTK")
plotDimRed(mouseBrainSubsetSCE, "PCA_logcounts")

compbiomed/singleCellTK documentation built on Feb. 10, 2024, 3:32 a.m.