Heatmap of GSEA result

Source: R/Plots.R

Heatmap of GSEA result

gseaHeatmap(
  SeuratObj,
  by = "GO",
  pathwayIDs = NULL,
  toshow = "-logFDR",
  topPath = 10,
  colour = "Greens",
  scale = "none",
  fontsize_row = 10,
  cluster_rows = TRUE,
  cluster_cols = TRUE
)

Arguments

SeuratObj

Seurat object
by

which GSEA result to show, one of "GO", "KEGG", "Reactome", "MSigDb", "WikiPathways", "DO", "NCG", "DGN"
pathwayIDs

pathway IDs to show. Default:NULL. If not NULL, parameter topPath becomes invalid.
toshow

which GSEA score to show, "-logFDR", "enrichmentScore", "NES", "pvalue", "p.adjust"
topPath

number of top pathways of each cluster to show
colour

color of heatmap, see RColorBrewer::brewer.pal.info
scale

if the values should be centered and scaled in either the row direction or the column direction, or none. Corresponding values are "row", "column" and "none"
fontsize_row

fontsize for rownames
cluster_rows

boolean values determining if rows should be clustered.
cluster_cols

boolean values determining if columns should be clustered.

Value

A Heatmap-class object.

Examples

if (FALSE) {
gseaHeatmap(SeuratObj, by = "GO", toshow = "-logFDR", topPath = 10, colour = "Greens")
}