topgo_trees: Print trees from topGO.

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Print trees from topGO.

Description

The tree printing functionality of topGO is pretty cool, but difficult to get set correctly.

Usage

topgo_trees(
  tg,
  score_limit = 0.01,
  sigforall = TRUE,
  do_mf_fisher_tree = TRUE,
  do_bp_fisher_tree = TRUE,
  do_cc_fisher_tree = TRUE,
  do_mf_ks_tree = FALSE,
  do_bp_ks_tree = FALSE,
  do_cc_ks_tree = FALSE,
  do_mf_el_tree = FALSE,
  do_bp_el_tree = FALSE,
  do_cc_el_tree = FALSE,
  do_mf_weight_tree = FALSE,
  do_bp_weight_tree = FALSE,
  do_cc_weight_tree = FALSE,
  parallel = FALSE
)

Arguments

tg	Data from simple_topgo().
score_limit	Score limit to decide whether to add to the tree.
sigforall	Add scores to the tree?
do_mf_fisher_tree	Add the fisher score molecular function tree?
do_bp_fisher_tree	Add the fisher biological process tree?
do_cc_fisher_tree	Add the fisher cellular component tree?
do_mf_ks_tree	Add the ks molecular function tree?
do_bp_ks_tree	Add the ks biological process tree?
do_cc_ks_tree	Add the ks cellular component tree?
do_mf_el_tree	Add the el molecular function tree?
do_bp_el_tree	Add the el biological process tree?
do_cc_el_tree	Add the el cellular component tree?
do_mf_weight_tree	Add the weight mf tree?
do_bp_weight_tree	Add the bp weighted tree?
do_cc_weight_tree	Add the guess
parallel	Perform operations in parallel to speed this up?

Value

Big list including the various outputs from topgo.

See Also

[topGO]

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.