Dear all,

I am using plotGOgraph() on enrichGO() results in clusterProfiler package. I read in the description of the plotGOgraph() function that rectangles represent significantly enriched categories:

Description

plot GO graph

Usage

plotGOgraph(x, firstSigNodes = 10, useInfo = "all", sigForAll = TRUE,
  useFullNames = TRUE, ...)

firstSigNodes

number of significant nodes (retangle nodes in the graph)

I guess that the colour indicates the adjusted pvalue level, but I cannot figured out what are the coloured circles.

If I remember well, I read somewhere that it was not possible to modify this figure. Am I right or is it possible to add a legend, at least for the colours?

Does this graph plot all the GO levels for the specified ontology?

Thank you,

Jane

The plotGOgraph function convert the enrichResult object to topGOdata object and use showSigOfNodes defined by topGO to visualize the GO topology. To my knowledge, topGO doesn't contain functionality to add a legend.  I am not sure whether this is possible. Maybe the author of topGO can helps.

Thank you for your answer.

Still, I cannot figured out what are the coloured circles. Only rectangles are supposed to represent significant categories. Neither the documentation of plotGOgraph, nor showSigOfNodes mentions the circles... Can you please explain what are the coloured circles?

Can you please confirm that colours indicate the adjusted pvalue level? It would be great to standardize the colours in the different graphs (dotplot, enrichmap and plotGOgraph). Do you think it could be possible, perhaps in future releases?