GOstats: Coloring nodes in the induced GO graph
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Tim Smith ★ 1.1k
@tim-smith-1532
Last seen 7.8 years ago
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@deepayan-sarkar-1436
Last seen 7.8 years ago
On 10/2/07, Tim Smith <tim_smith_666 at="" yahoo.com=""> wrote: > Hi, > > I looked at the documentation for GOstats and wanted to replicate the graph where different nodes are colored differently depending on their p-values. > > With the following code segment I can get the GO graph, but how do I color the nodes? > > ----------------------------------------------------------------- > library(Rgrahviz) > library(GOstats) > > g4 <- GOGraph(c("GO:0003680", "GO:0003701"), GOMFPARENTS) > plot(g4) > -------------------------------------------------------------------- ----------------- > > Also, is it possible to get the descriptive term (e.g.'AT binding' instead of "GO:0003680") in the graph? > Here's one way (adapting code from http://www.bioconductor.org/pub/docs/mogr/): node.attrs <- makeNodeAttrs(g4, shape="ellipse", label = substr(nodes(g4), 6, 10), fillcolor = sample(colors(), length(nodes(g4)))) plot(agopen(g4, recipEdges="distinct", layoutType="dot", nodeAttrs = node.attrs, name = "foo")) You would of course use more meaningful labels and colors in the call to makeNodeAttrs(). -Deepayan
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