plot_gsva_pca-ReactomeAnalysisResult-method: plot_gsva_pca - ReactomeAnalysisResult

Description Usage Arguments Value Examples

Description

Runs a Principal Component analysis (using prcomp) on the samples based on the pathway analysis results.

Usage

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## S4 method for signature 'ReactomeAnalysisResult'
plot_gsva_pca(object, pathway_ids = NULL, ...)

Arguments

object

A ReactomeAnalysisResult object containing a ssGSEA result

pathway_ids

A character vector of pathway ids. If set, only these pathways will be used for the PCA analysis.

...

Additional parameters are passed to prcomp

Value

A ggplot2 object representing the plot.

Examples

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# load the scRNA-seq example data
library(ReactomeGSA.data)
data(jerby_b_cells)

# perform the GSVA analysis
gsva_result <- analyse_sc_clusters(jerby_b_cells, verbose = FALSE)

reactome/ReactomeGSA documentation built on June 9, 2021, 10:07 a.m.