Relate Deconvolution Subgroups to Pathway Activities — compute.subgroup.pathways • multideconv

Correlates deconvolution subgroup profiles with a pre-computed pathway activity matrix and saves one heatmap per cell type to Results/. Use an external tool such as CellTFusion to compute pathway activity scores (e.g. PROGENy) before calling this function.

Usage

compute.subgroup.pathways(
  subgroups,
  pathways = NULL,
  file_name = "Test",
  height = 6,
  width = 12,
  par_mar = c(4, 25, 5, 3),
  pval = 0.05
)

Arguments

subgroups: Output list from compute.deconvolution.analysis().
pathways: A numeric matrix or data frame with samples as rows and pathway activities as columns. Row names must match sample identifiers in subgroups.
file_name: Character prefix used when naming output PDF files.
height: Plot height in inches (passed to ggplot2::ggsave()).
width: Plot width in inches (passed to ggplot2::ggsave()).
par_mar: Ignored; kept for backwards compatibility.
pval: P-value threshold; correlations above this are not starred.

Value

Invisibly returns NULL; side effects are PDF files in Results/.