Entering edit mode
Dear list,
I met problem in generate pdf file when use GeneAnswers. When open
"test.pdf" after xvfb-run following codes, it alerts "There was an
error opening this document. This file cannot be opened because it has
no pages."
How could I figure out this problem? Thanks.
$ xvfb-run R
...
> library(GeneAnswers)
Loading required package: igraph
Loading required package: RCurl
Loading required package: bitops
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation("pkgname")'.
Loading required package: XML
Loading required package: RSQLite
Loading required package: DBI
Loading required package: MASS
Loading required package: rgl
Loading required package: Heatplus
Loading required package: RColorBrewer
> data('humanGeneInput')
> data('humanExpr')
> x <- geneAnswersBuilder(humanGeneInput, 'org.Hs.eg.db',
categoryType='GO.BP', testType='hyperG', pvalueT=0.1,
FDR.correction=TRUE, geneExpressionProfile=humanExpr)
[1] "geneInput has built in ..."
Loading required package: org.Hs.eg.db
Loading required package: GO.db
[1] "annLib and categoryType have built in ..."
[1] "genesInCategory has built in ..."
[1] "Enrichment test is only performed based on annotated genes"
[1] "testType, pvalueT and enrichmentInfo have built in ..."
[1] "geneExpressionProfile has been built in ..."
[1] "GeneAnswers instance has been successfully created!"
> xx <- geneAnswersReadable(x)
[1] "Mapping geneInput ..."
[1] "Mapping genesInCategory ..."
[1] "Mapping enrichmentInfo rownames ..."
[1] "Mapping geneExprProfile rownames ..."
> pdf("~/test.pdf")
> geneAnswersChartPlots(xx,chartType="pieChart",newWindow=F)
> dev.off()
pdf
2
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] GO.db_2.5.0 org.Hs.eg.db_2.5.0 GeneAnswers_1.8.0
[4] RColorBrewer_1.0-2 Heatplus_1.22.0 rgl_0.92.798
[7] MASS_7.3-13 RSQLite_0.9-4 DBI_0.2-5
[10] XML_3.4-0 annotate_1.30.1 AnnotationDbi_1.14.1
[13] Biobase_2.12.1 RCurl_1.6-1 bitops_1.0-4.1
[16] igraph_0.5.5-2
loaded via a namespace (and not attached):
[1] graph_1.30.0 grid_2.13.0 RBGL_1.28.0
Rgraphviz_1.30.1
[5] tools_2.13.0 xtable_1.5-6
Yours sincerely,
Jianhong Ou
jianhong.ou at umassmed.edu