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?
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

```r
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