treemap_data {goat}

Construct tree and treemap data structures from geneset parent/child relations

Description

refer to the goat::treemap_plot() function for a complete example

Usage

treemap_data(
  geneset_ids,
  genesets,
  genesets_test_result,
  simplify = "none",
  toplevel_max_ngenes = NA
)

Arguments

geneset_ids

vector of geneset identifiers

genesets

entire geneset table; typically the complete GO database

genesets_test_result

geneset testing results; the output from test_genesets()

simplify

strategy for reducing the genesets returned in the treemap. Options; "leaf_only" (most stringent, returns only leafs in the tree structure) "prune_singletons" (remove parent terms that have exactly 1 child) "pvalue" (remove parent terms where the child term p-value is at least 4 times better) "none" (default; return all significant genesets that are not a "grouping term" in the treemap)

toplevel_max_ngenes

groups in the treemap should not have more than this many genes ('ngenes' in geneset test results). If not set, this defaults to 50% of the total number of unique genes in the geneset test results

Value

data structure needed for treemap_plot()