gostats_trees: Take gostats data and print it on a tree as topGO does.

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

Take gostats data and print it on a tree as topGO does.

Description

This shoehorns gostats data into a format acceptable by topgo and uses it to print pretty ontology trees showing the over represented ontologies.

Usage

gostats_trees(
  gostats_result,
  goid_map = "id2go.map",
  score_limit = 0.01,
  overwrite = FALSE,
  selector = "topDiffGenes",
  pval_column = "adj.P.Val"
)

Arguments

gostats_result	Return from simple_gostats().
goid_map	Mapping of IDs to GO in the Ramigo expected format.
score_limit	Maximum score to include as 'significant'.
overwrite	Overwrite the goid_map?
selector	Function to choose differentially expressed genes in the data.
pval_column	Column in the data to be used to extract pvalue scores.

Value

plots! Trees! oh my!

See Also

topGO gostats

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