plotReducedDimMC: Scater plotReducedDim for MCA like dimensionality Reduction

In RausellLab/CelliD: Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis

Scater plotReducedDim for MCA like dimensionality Reduction

Description

Small modification of the Scater plotReducedDim function to enable plotting features for mca like dimensionality reduction. Allows to represent a set of genes of interest on top of the regular cell scatter plot. The label of the genes can be iverlayed also but it is recommended to plot less than 50 genes label as it can overcrowd the plot severely.

Usage

plotReducedDimMC(
  X,
  reduction = "MCA",
  dims = c(1, 2),
  features = NULL,
  size.feature = 3,
  size.feature.text = 5,
  as.text = FALSE,
  ...
)

Arguments

X	a Single Cell Experiment Object
reduction	Which dimensionality reduction to use. If not specified, searches for mca.
dims	Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions
features	character vector of features to plot, must be present in the specified dimension loadings
size.feature	integer indicating size of geom_point for features
size.feature.text	integer indicating size of geom_text for features
as.text	logical indicating as to include text label for feature plotting, will produce warning if TRUE and length(features) > 50.
...	Other arguments passed to plotReducedDim

Value

A ggplot object

Examples

scePBMC <- as.SingleCellExperiment(seuratPbmc)
scePBMC <- RunMCA(scePBMC, nmcs = 5)
plotReducedDimMC(scePBMC)

RausellLab/CelliD documentation built on Jan. 12, 2024, 3:44 a.m.