cluster_trees: Take clusterprofile group data and print it on a tree as per...

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

Take clusterprofile group data and print it on a tree as per topGO.

Description

TopGO's ontology trees can be very illustrative. This function shoe-horns clusterProfiler data into the format expected by topGO and uses it to make those trees.

Usage

cluster_trees(
  de_genes,
  cpdata,
  goid_map = "id2go.map",
  go_db = NULL,
  score_limit = 0.2,
  overwrite = FALSE,
  selector = "topDiffGenes",
  pval_column = "adj.P.Val"
)

Arguments

de_genes	List of genes deemed 'interesting'.
cpdata	Data from simple_clusterprofiler().
goid_map	Mapping file of IDs to GO ontologies.
go_db	Dataframe of mappings used to build goid_map.
score_limit	Scoring limit above which to ignore genes.
overwrite	Overwrite an existing goid mapping file?
selector	Name of a function for applying scores to the trees.
pval_column	Name of the column in the GO table from which to extract scores.

Value

plots! Trees! oh my!

See Also

[Ramigo] [topGO::showSigOfNotes()]

Examples

## Not run: 
 cluster_data <- simple_clusterprofiler(genes, stuff)
 ctrees <- cluster_trees(genes, cluster_data)

## End(Not run)

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