Generates a heatmap for Progeny pathway scores, with optional sample annotations and customization options.
Usage
plot_progeny_heatmap(
progeny_scores,
annotations = NA,
annotation_prop = 0.1,
annotation_colors = NULL,
fname = NULL,
fwidth = 7,
fheight = 5,
...
)Arguments
- progeny_scores
A data frame of pathway scores or a `SummarizedExperiment` object containing pathway scores in its metadata.
- annotations
(Optional) Annotations for the samples to be displayed as tracks on the heatmap. Default is `NA`, meaning no annotations are used.
- annotation_prop
Proportion of the heatmap width allocated to annotations, if provided. Default is `0.1`.
- annotation_colors
(Optional) A named list of colors for the annotation tracks. Names must match the annotation variables.
- fname
(Optional) File name to save the heatmap as an image. If `NULL`, the heatmap is displayed but not saved. Default is `NULL`.
- fwidth
Width of the saved heatmap image in inches. Default is `7`.
- fheight
Height of the saved heatmap image in inches. Default is `5`.
- ...
Additional arguments passed to the internal heatmap plotting function.
Details
If `progeny_scores` is a data frame, it is assumed to contain pathway scores with row names as pathway names and column names as sample IDs. If it is a `SummarizedExperiment` object, pathway scores are extracted from the metadata under `progeny_scores`.
Annotations can be added to the heatmap if provided, and their appearance can be customized using `annotation_colors`.