[BioC] GO graphs made with topGO are unreadable

Sini [guest] guest at bioconductor.org
Fri Jan 18 08:50:32 CET 2013


Hello,

I've been using topGO to run enrichment analysis for gene sets and have used the showSigOfNodes command to make GO graphs of the enriched terms. Since the newest Bioconductor release in October, the text in the nodes of the GO graph has been unreadable. I have tried increasing the size of the picture, but that doesn't increase the resolution at all. Previously the graphs have looked just fine and this problem has occured after updating to the newest Bioconductor version. Any suggestions on how to fix this problem?

Best regards,
Sini

 -- output of sessionInfo(): 

> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] Rgraphviz_2.2.1      org.Hs.eg.db_2.8.0   KEGG.db_2.8.0        GOstats_2.24.0      
 [5] Category_2.24.0      topGO_2.10.0         SparseM_0.96         GO.db_2.8.0         
 [9] RSQLite_0.11.2       DBI_0.2-5            AnnotationDbi_1.20.3 Biobase_2.18.0      
[13] BiocGenerics_0.4.0   graph_1.36.1        

loaded via a namespace (and not attached):
 [1] annotate_1.36.0       AnnotationForge_1.0.3 genefilter_1.40.0     GSEABase_1.20.1      
 [5] IRanges_1.16.4        lattice_0.20-13       parallel_2.15.1       RBGL_1.34.0          
 [9] splines_2.15.1        stats4_2.15.1         survival_2.37-2       tools_2.15.1         
[13] XML_3.95-0.1          xtable_1.7-0         

--
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