plot_enrichment

Plot the result of run_enrichment function as a heatmap.

plot_enrichment(
  x,
  group.by = "cluster",
  direction = c("Up", "Down"),
  FDR = 0.01,
  col_up = c("white", "red"),
  col_down = c("white", "blue"),
  top_ann = NULL,
  circle.scale = 0.2,
  cluster_columns = FALSE,
  border = TRUE,
  padding = NULL,
  ...
)

Arguments

x

data.frame with results from run_enrichment.

group.by

grouping variable (default: cluster).

direction

which direction ("Up", "Down") to plot for enrichment (default: c("Up", "Down")).

FDR

cutoff to select significantly enriched terms/pathways.

col_up

colors to use for Up and passed down to ComplexHeatmap::Heatmap.

col_down

colors to use for Down and passed down to ComplexHeatmap::Heatmap.

top_ann

top annotations passed down to ComplexHeatmap::Heatmap.

circle.scale

scale to be applied to the circles.

cluster_columns

whether to cluster columns.

border

whether to add border.

padding

padding around heatmap passed down to ComplexHeatmap::draw.

...

additional arguments passed down to ComplexHeatmap::Heatmap.