gg_panelplot: Create a tmod panel plot using ggplot

In bihealth/bioshmods: What the Package Does (One Line, Title Case)

Create a tmod panel plot using ggplot

Description

Create a tmod panel plot using ggplot

Usage

gg_panelplot(
  res,
  pie,
  auc_thr = 0.5,
  q_thr = 0.05,
  filter_row_q = 0.01,
  filter_row_auc = 0.65,
  q_cutoff = 1e-12,
  label_angle = 45,
  cleanup = TRUE,
  add_ids = TRUE
)

Arguments

res	a list with tmod results (each element of the list is a data frame returned by a tmod test function)
pie	a list with summaries of significantly DE genes by gene set. Each a element of the list is a matrix returned by tmodDecideTests.
auc_thr	gene sets enrichments with AUC below auc_thr will not be shown
q_thr	gene sets enrichments with q (adjusted P value) above q_thr will not be shown
filter_row_q	Gene sets will only be shown if at least in one contrast q is smaller than filter_row_q
filter_row_auc	Gene sets will only be shown if at least in one contrast AUC is larger than filter_row_q
q_cutoff	Any q value below q_cutoff will be considered equal to q_cutoff
label_angle	The angle at which column labels are shown
cleanup	attempt to clean up gene set titls
add_ids	add IDs of gene sets to their titles on the plot

bihealth/bioshmods documentation built on July 1, 2023, 4:32 a.m.