createEnrichMap: Using functional enrichment results in gprofiler2 format to...

In adeschen/gprofiler2cytoscape: From functional enrichment results to biological networks

Using functional enrichment results in gprofiler2 format to create an enrichment map

Description

User selected enrichment terms are used to create an enrichment map. The selection of the term can by specifying by the source of the terms (GO:MF, REAC, TF, etc...) or by listing the selected term IDs. The map is only generated when there is at least on significant term to graph.

Usage

createEnrichMap(
  gostObject,
  query,
  source = c("TERM_ID", "GO:MF", "GO:CC", "GO:BP", "KEGG", "REAC", "TF", "MIRNA", "HPA",
    "CORUM", "HP", "WP"),
  termIDs = NULL,
  removeRoot = TRUE,
  showCategory = 30L,
  groupCategory = FALSE,
  categoryLabel = 1,
  categoryNode = 1,
  line = 1,
  force = TRUE
)

Arguments

gostObject	a list corresponding to gprofiler2 enrichment output that contains and that contains the results from an enrichment analysis.
query	a character string representing the name of the query that is going to be used to generate the graph. The query must exist in the gostObject object.
source	a character string representing the selected source that will be used to generate the network. To hand-pick the terms to be used, "TERM_ID" should be used and the list of selected term IDs should be passed through the termIDs parameter. The possible sources are "GO:BP" for Gene Ontology Biological Process, "GO:CC" for Gene Ontology Cellular Component, "GO:MF" for Gene Ontology Molecular Function, "KEGG" for Kegg, "REAC" for Reactome, "TF" for TRANSFAC, "MIRNA" for miRTarBase, "CORUM" for CORUM database, "HP" for Human phenotype ontology and "WP" for WikiPathways. Default: "TERM_ID".
termIDs	a vector of character strings that contains the term IDS retained for the creation of the network. Default: NULL.
removeRoot	a logical that specified if the root terms of the selected source should be removed (when present). Default: TRUE.
showCategory	a positive integer or a vector of characters representing terms. If a integer, the first n terms will be displayed. If vector of terms, the selected terms will be displayed. Default: 30L.
groupCategory	a logical indicating if the categories should be grouped. Default: FALSE.
categoryLabel	a positive numeric representing the amount by which plotting category nodes label size should be scaled relative to the default (1). Default: 1.s
categoryNode	a positive numeric representing the amount by which plotting category nodes should be scaled relative to the default (1). Default: 1.
line	a non-negative numeric representing the scale of line width. Default: 1.
force	a logical indicating if the repulsion between overlapping text labels should be forced. Default: TRUE.

Value

a ggplot object which is the enrichment map for enrichment results.

Author(s)

Astrid Deschênes

Examples

## Loading dataset containing result from an enrichment analysis done with
## gprofiler2
data(parentalNapaVsDMSOEnrichment)

## Extract query information (only one in this dataset)
query <- unique(parentalNapaVsDMSOEnrichment$result$query)

## Create graph for Gene Ontology - Cellular Component related results
createEnrichMap(gostObject=parentalNapaVsDMSOEnrichment, 
    query=query, source="GO:CC", removeRoot=TRUE)

adeschen/gprofiler2cytoscape documentation built on April 26, 2024, 9:33 p.m.