clusterProfiler-diagram.R

library("DiagrammeR")


grViz("digraph course {
rankdir = LR
node [shape = box, style=filled, fontsize=25]
layout = dot
compound =true
#color = crimson

subgraph clusterA{
fontsize = 30
label = 'ChIPseeker'
style = dashed
rank = same

roi [label = 'Region of interest']
gene2 [label = 'Gene in proximity']

}

subgraph clusterB{
fontsize = 30

rankdir = LR
label = 'Over Representation Analysis'
style = dashed
rank = same

subgraph cluster0 {
label = 'clusterProfiler'

enrichGO
enrichKEGG 
enrichMKEGG
enricher [label = 'enricher\nfor MSigDb, wikiPathway\nand many others']
}

subgraph cluster1 {
label = 'DOSE'

enrichDO
enrichNCG
enrichDGN
}


subgraph cluster2 {
label = 'ReactomePA'

enrichPathway
}

subgraph cluster3 {
label = 'meshes'

enrichMeSH
}


}



subgraph clusterC{
fontsize = 30

label = 'Gene Set Enrichment Analysis'
style = dashed
rank = same


subgraph cluster0 {
label = 'clusterProfiler'

gseGO
gseKEGG 
gseMKEGG
GSEA [label = 'GSEA\nfor MSigDb, wikiPathway\nand many others']
}

subgraph cluster1 {
label = 'DOSE'

gseDO
gseNCG
gseDGN
}


subgraph cluster2 {
label = 'ReactomePA'

gsePathway
}

subgraph cluster3 {
label = 'meshes'

gseMeSH
}

}



subgraph clusterD{
fontsize = 30

label = 'Visualization using enrichplot'
style = dashed
rank = same

subgraph cluster1 {
label = 'ORA only'
barplot
goplot
}

subgraph cluster2 {
label = 'ORA & GSEA'
dotplot
upsetplot
heatplot
cnetplot
emapplot
}

subgraph cluster3 {
label = 'GSEA only'
gseaplot
gseaplot2
gsearank
ridgeplot
}

}


subgraph clusterE{
fontsize = 30
label = 'Remove redundant terms'
style = dashed
rank = same

simplify [label = 'simplify for GO only\nby GOSemSim']
}

subgraph clusterF{
fontsize = 30

label = 'Compare different conditions'
style = dashed
rank = same

comparecluster [label = 'compareCluster\nby clusterProfiler']
}


subgraph clusterG{
fontsize = 30

label = 'Measuring semantic Similarites'
style = dashed
rank = same

gosemsim [label = 'based on Gene Ontology by GOSemSim']
dosim [label = 'based on Disease Ontology by DOSE']
meshsim [label = 'based on Medical Subject Headings by meshes']
}

rnaseq [label = 'RNA-seq']
gene [label = 'Gene of interest\ne.g. from pull-down']
genelist [label='Ranked gene list']
de [label = 'Differential expressed gene']
roi->gene2
#ora [label = 'Over Representation Analysis']
#gsea [label = 'Gene Set Enrichment Analysis']
microarray -> de
rnaseq -> de
microarray -> genelist #gseKEGG[lhead=clusterC]
rnaseq -> genelist
de -> enrichKEGG[lhead=clusterB]
gene -> enrichKEGG[lhead=clusterB]
gene2 -> enrichKEGG[lhead=clusterB]
enrichKEGG -> enrichNCG [style = invis]
enrichPathway -> enrichMeSH  [style = invis]
gseKEGG -> gseNCG [style = invis]
gsePathway -> gseMeSH  [style = invis]
genelist -> gseMKEGG [lhead=clusterC]
others [label = 'Other sources']

others -> genelist
enrichDGN -> barplot [ltail=clusterB]
enrichDGN -> dotplot [ltail=clusterB]
enrichDGN -> upsetplot [ltail=clusterB]
enrichDGN -> heatplot [ltail=clusterB]
enrichDGN -> cnetplot [ltail=clusterB]
enrichDGN -> emapplot [ltail=clusterB]
enrichGO -> goplot

gseDGN -> ridgeplot [ltail=clusterC]
gseDGN -> dotplot [ltail=clusterC]
gseDGN -> upsetplot [ltail=clusterC]
gseDGN -> heatplot [ltail=clusterC]
gseDGN -> cnetplot [ltail=clusterC]
gseDGN -> emapplot [ltail=clusterC]
gseDGN -> gseaplot [ltail=clusterC]
gseDGN -> gseaplot2 [ltail=clusterC]
gseDGN -> gsearank [ltail=clusterC]

comparecluster -> dotplot 
comparecluster -> cnetplot
comparecluster -> emapplot

enrichGO -> simplify
gseGO -> simplify

enrichDO -> comparecluster [lhead=clusterF, ltail=clusterB]
#enrichNCG -> comparecluster
#enrichDGN -> comparecluster
#enrichGO -> comparecluster
#enrichKEGG -> comparecluster
#enrichPathway -> comparecluster
#enricher -> comparecluster
#enrichMeSH -> comparecluster[ltail=clusterF]


gene2 -> gosemsim [lhead=clusterG]
de -> gosemsim [lhead=clusterG]
gene -> gosemsim[lhead=clusterG]
}")  -> x

x

#yyplot::gv2file(x,  file = 'clusterProfiler.pdf')
yyplot::gv2file(x, file = 'figures/clusterProfiler-diagram.png' )