R/pkgdiagram.R

In ViSEAGO: ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity

#' @title Display the ViSEAGO package diagram.
#' @description This function build the ViSEAGO package diagram available displayed in the vignette.
#' @importFrom DiagrammeR grViz
#' @param x rectangles colors for the five subgraphs with all white by defaults
#' @details This function use \pkg{DiagrammeR} package \code{\link[DiagrammeR]{grViz}} to display the ViSEAGO methods diagram with colored or not subgraphs rectangles.
#' @references
#' Knut Sveidqvist, Mike Bostock, Chris Pettitt, Mike Daines, Andrei Kashcha and Richard Iannone (2017). DiagrammeR: Create Graph Diagrams and Flowcharts Using R.
#' R package version 0.9.0. https://CRAN.R-project.org/package=DiagrammeR.
#' @return an html diagram
#' @examples
#' # print diagram without focus
#' ViSEAGO::pkgdiagram(x=c("white","white","white","white","white"))
#'
#' # print diagram with focus one the gene list
#' ViSEAGO::pkgdiagram(x=c("black","white","white","white","white"))
#'
#' # print diagram with a focus on the annotation step
#' ViSEAGO::pkgdiagram(x=c("white","black","white","white","white"))
#'
#' # print diagram with a focus on the enrichment step
#' ViSEAGO::pkgdiagram(x=c("white","white","black","white","white"))
#'
#' # print diagram with a focus on the Semantic Similarity step
#' ViSEAGO::pkgdiagram(x=c("white","white","white","black","white"))
#'
#' # print diagram with focus on the visualization step
#' ViSEAGO::pkgdiagram(x=c("white","white","white","white","black"))
#' @keywords internal
#' @export
pkgdiagram<-function(x=c("white","white","white","white","white")){

    # print the diagram
    grViz(
        diagram=paste("
            # init the graph
            digraph ViSEAGO_map {

                # a 'graph' statement
                graph [layout = dot,overlap = false, fontsize = 10, splines= true, shape =oval,fixedsize = true,width = 2.5,fontname = Helvetica]

                node [fillcolor=MistyRose2,style=filled]
                subgraph cluster0 {
                    label='List(s) of genes'
                    fontsize = 25
                    fontcolor = MistyRose2
                    labelloc=t
                    color=",x[1],"
                    'Genes of interest \n and background'
                    'preranked gene set with \nthe statistical values used'
                }

                node [fillcolor=orange,style=filled]
                subgraph cluster1 {
                    label='Genomic ressources'
                    fontsize = 25
                    fontcolor = orange
                    labelloc=t
                    color=",x[2],"
                    Bioconductor2GO
                    EntrezGene2GO
                    Ensembl2GO
                    Uniprot2GO
                    Custom2GO
                    available_organisms
                    annotate
                }

                node [fillcolor=lightblue1,style=filled]
                subgraph cluster2 {
                    label='Enrichment tests'
                    fontsize = 25
                    fontcolor =lightblue1
                    labelloc=t
                    color=",x[3],"
                    create_topGOdata
                    RunTest
                    runfgsea
                    merge_enrich_terms
                }

                node [fillcolor=LightCoral,style=filled]
                subgraph cluster3 {
                    label='Visualization'
                    fontsize = 25
                    fontcolor = LightCoral
                    labelloc=t
                    color=",x[5],"
                    show_table
                    show_heatmap
                    GOcount
                    Upset
                    MDSplot
                    GOterms_heatmap
                    GOclusters_heatmap
                    compare_clusters
                }

                node [fillcolor=LimeGreen,style=filled]
                subgraph cluster4 {
                    label='GO Semantic Similarities'
                    fontsize = 25
                    fontcolor = LimeGreen
                    labelloc=t
                    color=",x[4],"
                    build_GO_SS
                    compute_SS_distances
                }

                # 'edge' statements
                'Genes of interest \n and background'-> create_topGOdata
                'preranked gene set with \nthe statistical values used' -> runfgsea
                Bioconductor2GO->annotate
                EntrezGene2GO->annotate
                Ensembl2GO->annotate
                Uniprot2GO->annotate
                Custom2GO->annotate
                annotate->create_topGOdata
                annotate->runfgsea
                create_topGOdata-> {RunTest merge_enrich_terms}
                RunTest->merge_enrich_terms
                runfgsea->merge_enrich_terms
                merge_enrich_terms->{build_GO_SS show_table GOcount Upset}
                build_GO_SS->{compute_SS_distances show_table GOcount Upset}
                compute_SS_distances->{GOcount MDSplot Upset GOterms_heatmap GOclusters_heatmap}
                GOterms_heatmap->{compute_SS_distances show_table show_heatmap compare_clusters}
                GOclusters_heatmap->{show_table show_heatmap MDSplot}
                Bioconductor2GO->available_organisms
                EntrezGene2GO->available_organisms
                Ensembl2GO->available_organisms
                Uniprot2GO->available_organisms
                Custom2GO->available_organisms
            }",
            sep=""
        )
    )
}