[BioC] question about xvfb-run GeneAnswers

[James W. MacDonald]

Hi Jianhong Ou,

On 9/30/2011 9:40 AM, Ou, Jianhong wrote:
> 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()

Just a shot in the dark here, but don't you want newWindow = TRUE?

Best,

Jim


> 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
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826

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