plotReducedDimMC: Scater plotReducedDim for MCA like dimensionality Reduction

Description Usage Arguments Value Examples

View source: R/visualisation.R

Description

Small modification of the Scater plotReducedDim function to enable plotting features for mca like dimensionality reduction.

Usage

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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

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

Cortalak/cellID documentation built on Aug. 3, 2020, 9:01 p.m.