plot_heatmap_hcl: Draw a clustered heatmap of the radiomic dataset

In cgplab/RadAR: Radiomic Analysis with R

Description

This function uses pheatmap to draw a heatmap of feature values (rows) across samples (columns). The rows and columns of the heatmap are ordered based on previous required hierarchical clustering generated by do_hierarchical_clustering. Dendrograms for columns and rows are also reported with optional annotation tracks.

Usage

plot_heatmap_hcl(
  rdr = NULL,
  show_feature_names = F,
  show_sample_names = F,
  annotation_tracks = NULL,
  annotation_data = NULL,
  annotation_colors = NULL,
  ncolors = 50,
  save_plot_to = NULL,
  width_plot = 20,
  height_plot = 15
)

Arguments

rdr	A RadAR object (class SummarizedExperiment).
show_feature_names	(logical) Should feature names be displayed in the heatmap?
show_sample_names	(logical) Should sample names be displayed in the heatmap?
annotation_tracks	(character) Tracks to report in the annotation section of the heatmap. Available annotation tracks can be obtained by names(colData(rdr)).
annotation_data	(data.frame) A data frame specifying tracks to report in the annotation section. For more details refer to ?pheatmap::pheatmap.
annotation_colors	(list) List for specifying annotation_col track colors manually.For more details and examples refer to ?pheatmap::pheatmap.
ncolors	(integer) Number of colors of the color palette.
save_plot_to	(character) If specified, filename where the heatmap will be saved to.
width_plot	(numeric) output file width in inches.
height_plot	(numeric) output file height in inches.

Value

none

Author(s)

Matteo Benelli ([e-mail])

cgplab/RadAR documentation built on Nov. 10, 2021, 1:32 a.m.