DimPlotMC: Seurat DimPlot for MCA like Dimensionality Reduction

Description Usage Arguments Value Examples

View source: R/visualisation.R

Description

Small modification of the regular Seurat DimPlot function to enable plotting features for mca like dimensionality reduction.

Usage

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

Arguments

X

a seurat 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 DimPlot

Value

A ggplot object

Examples

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seuratPbmc <- RunMCA(seuratPbmc, nmcs = 30)
seuratPbmc <- DimPlotMC(seuratPbmc, nmcs = 30, features = Seurat::VariableFeatures(seuratPbmc))

cbl-imagine/cellID documentation built on Nov. 12, 2019, 1:36 a.m.