Question

How to produce png files from printGraph

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mictadlo ▴ 10

@mictadlo-10885

Last seen 4.9 years ago

Hi, Is there a way that printGraph produces png files?

showSigOfNodes(sampleGOdata, 
               score(resultKS.elim), 
               firstSigNodes = 5, 
               useInfo='all')

printGraph(sampleGOdata, 
           resultKS.elim, 
           firstSigNodes = 5, 
           fn.prefix = paste(comparisons,"-goNodes"), 
           useInfo = "all", 
           pdfSW = TRUE)

Thank you in advance.

topgo • 2.3k views

ADD COMMENT • link updated 7.2 years ago by arendsee ▴ 10 • written 7.2 years ago by mictadlo ▴ 10

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In your code, you need to declare the variables 'sampleGOdata', 'resultKS.elim', and 'comparisons'. Also you need to include all import statements (e.g. 'library(topGO)'). You should be able to just paste the code example into an R shell and have it run.

ADD REPLY • link 7.2 years ago arendsee ▴ 10

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Yes, the code runs and produces a pdf file but how to change it that it produces png rather than pdf file?

ADD REPLY • link 7.2 years ago mictadlo ▴ 10

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Yes, but I can't run the code. No one else can either. The variables 'sampleGOdata', 'resultKS.elim', and 'comparison' are not defined. I had to look up the topGO vignette to find the definitions of 'sampleGOdata' and 'resultKS.elim'. But still I don't know what 'comparisons' is. How is 'comparisons' declared in your code?

ADD REPLY • link 7.2 years ago arendsee ▴ 10

score 0 · Answer 1 · 2017-10-05

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arendsee ▴ 10

@arendsee-14118

Last seen 7.2 years ago

Iowa State University

Here is a complete example:

library(topGO)
library(ALL)
data(geneList)
sampleGOdata <- new("topGOdata",
                    description = "Simple session", ontology = "BP",
                    allGenes = geneList, geneSel = topDiffGenes,
                    nodeSize = 10,
                    annot = annFUN.db, affyLib = affyLib)

resultKS.elim <- runTest(sampleGOdata, algorithm = "elim", statistic = "ks")

png("sampleGOdata.png")
showSigOfNodes(sampleGOdata, 
               score(resultKS.elim), 
               firstSigNodes = 5, 
               useInfo='all')
dev.off()

The functions printGraph and showSigOfNodes do the same thing, except that printGraph automatically makes a PDF or PS file.

I don't have enough rep to write another comment, so I'll have to just edit my answer. If you want better resolution, you might try reading this blog post.

If this was helpful, you I'd appreciate it if you upvote the answer (then maybe I'll be able to write more than 5 comments a day).

ADD COMMENT • link 7.2 years ago arendsee ▴ 10

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Although, your example isn't quite complete. I don't know offhand what package `showSigOfNodes` is from, so I can't immediately replicate your code. You should add the import statements (e.g. `library(whatever)`). I assume that `printGraph` is producing a figure of some sort?

ADD REPLY • link 7.2 years ago arendsee ▴ 10

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It is library(topGO) and I follow the instruction from there manual.

ADD REPLY • link 7.2 years ago mictadlo ▴ 10

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Unfortunately, it did not work and I only got in terminal

png
3

What did I miss?

ADD REPLY • link 7.2 years ago mictadlo ▴ 10

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Thank you, but how is it possible to improve the resolution?


> png("~/sampleGOdata.png", res = 300)
> showSigOfNodes(sampleGOdata,
+                score(resultKS.elim),
+                firstSigNodes = 5,
+                useInfo='all')
Error in plot.new() : figure margins too large

ADD REPLY • link 7.2 years ago mictadlo ▴ 10