plot_heatmaps: plots the heatmaps from training_and_test_model (see Boniolo...

In biomedbigdata/SPONGE: Sparse Partial Correlations On Gene Expression

plots the heatmaps from training_and_test_model (see Boniolo and Hoffmann 2022 et al. Fig. 6)

Description

plots the heatmaps from training_and_test_model (see Boniolo and Hoffmann 2022 et al. Fig. 6)

Usage

plot_heatmaps(
  trained_model,
  spongEffects,
  meta_data,
  label,
  sampleIDs,
  Modules_to_Plot = 10,
  show.rownames = T,
  show.colnames = F,
  title
)

Arguments

trained_model	returned from train_and_test_model
spongEffects	output of enrichment_modules()
meta_data	metadata of samples (retrieved from prepare_tcga_for_spongEffects() or from prepare_metabric_for_spongEffects())
label	Column of metadata to use as label in classification model
sampleIDs	Column of metadata containing sample/patient IDs to be matched with column names of spongEffects scores
Modules_to_Plot	Number of modules to plot in the heatmap. Default = 2
show.rownames	Add row names (i.e. module names) to the heatmap. Default = F
show.colnames	Add column names (i.e. sample names) to the heatmap. Default = F

Value

ComplexHeatmap object NOT FUNCTIONAL

biomedbigdata/SPONGE documentation built on Feb. 6, 2023, 10:19 p.m.