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topGO use showSigOfNodes for non-topGO data? or: how to visualize GO graph from GOseq

The topGO package appears to have a function showSigOfNodes, which plots the GO graph and highlights the enriched terms. I have done my GO enrichment analysis with GOseq and that packages doesn't provide a plot function like that. Is there any way the function from topGO can be made to accept the data from GOseq?

If not, what else should be used? I know REVIGO and it's nice but it shows graphs based on semantic similarity, not the GO hierarchy.

Is there anything else available in R/bioconductor?

topgo bioconductor goseq rna-seq r
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updated by Ram Ram • written by tospo • tospo

2 answers

If you just want to view the hierarchy of the GO with provided GOids, you can have a try the combination of function makeGOGraph from package AnnotationDbi and plotGOTermGraph from GOstats.

UPDATE: 20170510

goIDs <- c("GO:0051130","GO:0019912","GO:0005783")
color <- c("lightblue","red","yellow")
pv <- c(0.0001,0.03,1e-10)

## get results
pp <- getAmigoTree(goIDs=goIDs,color=color,filename="example",picType="png",pvalues=pv)

The graph can be get from: http://pan.baidu.com/s/1c2lEkxy

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updated by Ram Ram • written by pengchy pengchy

Another choice is RamiGO bioconductor package. But it need to visit AmiGO website.

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written by pengchy pengchy

To my knowledge there isn't anything directly available in bioconductor. AmiGO has some tools and I think they have an API. For our iPathwayGuide, we had to develop and create our own visualization tool that allows users to explore the GO graph. If you want to check it out, it's free to try. All you need is an experiment with Gene ID, logFC, and p-value and you can go forward.

Here's a screenshot of the GO analysis we provide.

screenshot of our GO analysis

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updated by Ram Ram • written by andrew andrew

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