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
    )

[Package clustifyr version 1.6.0 Index]