createMultiEmap: Create a basic enrichment map

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

Create a basic enrichment map

Description

The function creates a basic enrichment map using functional enrichment results.

Usage

createMultiEmap(
  gostResultsList,
  queryList,
  showCategory,
  groupCategory,
  categoryLabel,
  categoryNode,
  line,
  force
)

Arguments

gostResultsList	a list of data.frame containing the enrichment results to be plot with different group identification.
queryList	a list of character string representing the name of query retained for each enrichment results present in the gostResultsList parameter. The query should be present in its associated enrichment results.
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.
groupCategory	a logical indicating if the categories should be grouped.
categoryLabel	a positive numeric representing the amount by which plotting category nodes label size should be scaled relative to the default (1).
categoryNode	a positive numeric representing the amount by which plotting category nodes should be scaled relative to the default (1).
line	a non-negative numeric representing the scale of line width.
force	a logical indicating if the repulsion between overlapping text labels should be forced.

Value

a ggplot object representing the enrichment map with different colors for each group of enrichment results.

Author(s)

Astrid Deschênes

Examples

## Load the result of an enrichment analysis done with gprofiler2
data(parentalNapaVsDMSOEnrichment)

## Only retain the results section
gostResults <- as.data.frame(parentalNapaVsDMSOEnrichment$result)

## Limit the results subsection of REACTOME and KEGG
gostResultsREAC <- gostResults[which(gostResults$source == "REAC"),]
gostResultsREAC <- gostResultsREAC[1:13, ]
gostResultsKEGG <- gostResults[which(gostResults$source == "KEGG"),]

## Extract meta data information
queryList <- list("parental - REACTOME", "parental - KEGG")

## Create basic enrichment map using Wikipathways terms
enrichViewNet:::createMultiEmap(gostResultsList=list(gostResultsREAC, 
    gostResultsKEGG), queryList=queryList, showCategory=30L, 
    groupCategory=FALSE, categoryLabel=1, categoryNode=1, line=1.4, 
    force=TRUE)
    

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