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

Source: R/methodsEmap.R
createEnrichMapAsIgraph.Rd

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. The output is an igraph.

Usage

createEnrichMapAsIgraph(
  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,
  similarityCutOff = 0.2
)

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 representing the maximum number of terms to display. If a integer, the first n terms will be displayed. If NULL, all terms will be displayed. Default: 30L.

similarityCutOff

a positive numeric between 0 and 1 indicating the minimum level of similarity between two terms to have an edge linking the terms. Default: 0.20.

Value

a igraph object which is the enrichment map for enrichment results. The node have 2 attributes: "name" and "size". The "name" corresponds to the term description. While the "size" corresponds to the number of genes found in the specific gene set. The edges have 3 attributes: "similarity", "width", and "weight". All those 3 attributes correspond to the Jaccard coefficient.

Author

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
mapG <- createEnrichMapAsIgraph(gostObject=parentalNapaVsDMSOEnrichment, 
    query=query, source="GO:CC", removeRoot=TRUE, 
    showCategory=30L, similarityCutOff=0.20)

## Required library igraph to show the graph
if(requireNamespace("igraph", quietly=TRUE)) {
    ## Using library igraph to show the graph
    library(igraph)
    plot(mapG)
}
#> 
#> Attaching package: ‘igraph’
#> The following objects are masked from ‘package:stats’:
#> 
#>     decompose, spectrum
#> The following object is masked from ‘package:base’:
#> 
#>     union


if (requireNamespace("ggplot2", quietly=TRUE) &&
        requireNamespace("igraph", quietly=TRUE) &&
        requireNamespace("ggtangle", quietly=TRUE) &&
        requireNamespace("ggnetwork", quietly=TRUE)) {
    ## Using more complex set of libraries to display personalized graph
    library(ggplot2)
    library(igraph)
    library(ggnetwork)
    library(ggtangle)
    emapG <- ggplot(mapG, layout=layout_with_fr) +
                geom_edge(color="gray", linewidth=1) + 
                geom_nodes(aes(size=size)) + 
                geom_nodetext(aes(label=name), color="black", size=3) +
                theme_void()
    emapG
}
#> Registered S3 method overwritten by 'ggnetwork':
#>   method         from  
#>   fortify.igraph ggtree
#> ggtangle v0.0.9 Learn more at https://yulab-smu.top/
#>