plot_pathway_gsea {clustifyr}

R Documentation

plot GSEA pathway scores as heatmap, returns a list containing results and plot.

Description

plot GSEA pathway scores as heatmap, returns a list containing results and plot.

Usage

plot_pathway_gsea(
  mat,
  pathway_list,
  n_perm = 1000,
  scale = TRUE,
  topn = 5,
  returning = "both"
)

Arguments

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

Value

list of matrix and plot, or just plot, matrix of GSEA NES values, cell types as row names, pathways as column names

Examples

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
)

---