plot_pathway_gsea {clustifyr} | R Documentation |
plot GSEA pathway scores as heatmap, returns a list containing results and plot.
plot_pathway_gsea( mat, pathway_list, n_perm = 1000, scale = TRUE, topn = 5, returning = "both" )
mat |
expression matrix |
pathway_list |
a list of vectors, each named for a specific pathway, or dataframe |
n_perm |
Number of permutation for fgsea function. Defaults to 1000. |
scale |
convert expr_mat into zscores prior to running GSEA?, default = TRUE |
topn |
number of top pathways to plot |
returning |
to return "both" list and plot, or either one |
list of matrix and plot, or just plot, matrix of GSEA NES values, cell types as row names, pathways as column names
gl <- list( "n" = c("PPBP", "LYZ", "S100A9"), "a" = c("IGLL5", "GNLY", "FTL") ) pbmc_avg <- average_clusters( mat = pbmc_matrix_small, metadata = pbmc_meta, cluster_col = "classified" ) plot_pathway_gsea( pbmc_avg, gl, 5 )