This function generates a heatmap of pathway scores, with optional sample annotations.
Usage
plot_pathway_heatmap(
pathway_scores,
pathways = 1:20,
annotations = NA,
annotation_prop = 0.1,
annotation_colors = NULL,
fname = NULL,
fwidth = 7,
fheight = 5,
...
)Arguments
- pathway_scores
Either a data frame of pathway scores or a SummarizedExperiment object containing pathway scores in its metadata.
- pathways
A vector specifying the pathways to include in the heatmap. Defaults to the first 20 pathways.
- annotations
Optional. Sample annotations to include in the heatmap. Defaults to NA.
- annotation_prop
A numeric value specifying the proportion of the heatmap allocated to annotations. Defaults to 0.1.
- annotation_colors
Optional. A list of colors for annotations. Defaults to NULL.
- fname
Optional. A character string specifying the file name to save the heatmap. Defaults to NULL.
- fwidth
Numeric. The width of the saved heatmap file. Defaults to 7.
- fheight
Numeric. The height of the saved heatmap file. Defaults to 5.
- ...
Additional parameters passed to the heatmap plotting function.