cummeRbund graphics not working
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@sabet-julia-a-6404
Last seen 10.2 years ago
Hello all, I have been trying to use cummeRbund for a long time but I have not been able to get the graphics (plots) to show up either by "windows()" or by making a pdf file. I am using R on windows. I am pretty new to R so I am not sure if this is a general R issue or some issue specific to this package. I have been able to generate plots in other packages... This is the code that I used: >install.packages("RSQLite") >install.packages("ggplot2") >install.packages("reshape2") >install.packages("plyr") >install.packages("fastcluster") >source("http://bioconductor.org/biocLite.R") >biocLite("rtracklayer") >biocLite("Gviz") >biocLite("cummeRbund") > setwd("C:/Users/jtoman01/Desktop/RNA Seq/combinedsexcuffdiff7.24") > cuff_data <- readCufflinks() > annot <- read.table("gene_exp.diff",sep="\t",header=T,na.string="-") > addFeatures(cuff_data,annot,level="genes") > windows() > disp<-dispersionPlot(genes(cuff_data)) > pdf("dispersion.pdf") > disp<-dispersionPlot(genes(cuff_data)) > dev.off() As far as warnings or errors, this was the only thing, which showed up after "cuff_data <- readCufflinks()": Warning messages: 1: attributes are not identical across measure variables; they will be dropped 2: attributes are not identical across measure variables; they will be dropped 3: attributes are not identical across measure variables; they will be dropped 4: attributes are not identical across measure variables; they will be dropped 5: attributes are not identical across measure variables; they will be dropped 6: attributes are not identical across measure variables; they will be dropped 7: attributes are not identical across measure variables; they will be dropped 8: attributes are not identical across measure variables; they will be dropped Here is my sessionInfo(): R version 3.1.1 (2014-07-10) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] grid parallel stats graphics grDevices utils datasets methods base other attached packages: [1] cummeRbund_2.6.1 Gviz_1.8.4 rtracklayer_1.24.2 GenomicRanges_1.16.3 GenomeInfoDb_1.0.2 IRanges_1.22.9 [7] BiocGenerics_0.10.0 fastcluster_1.1.13 plyr_1.8.1 reshape2_1.4 ggplot2_1.0.0 RSQLite_0.11.4 [13] DBI_0.2-7 BiocInstaller_1.14.2 loaded via a namespace (and not attached): [1] AnnotationDbi_1.26.0 BatchJobs_1.3 BBmisc_1.7 Biobase_2.24.0 BiocParallel_0.6.1 [6] biomaRt_2.20.0 Biostrings_2.32.1 biovizBase_1.12.1 bitops_1.0-6 brew_1.0-6 [11] BSgenome_1.32.0 checkmate_1.2 cluster_1.15.2 codetools_0.2-8 colorspace_1.2-4 [16] dichromat_2.0-0 digest_0.6.4 fail_1.2 foreach_1.4.2 Formula_1.1-2 [21] GenomicAlignments_1.0.3 GenomicFeatures_1.16.2 gtable_0.1.2 Hmisc_3.14-4 iterators_1.0.7 [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-33 matrixStats_0.10.0 munsell_0.4.2 [31] proto_0.3-10 R.methodsS3_1.6.1 RColorBrewer_1.0-5 Rcpp_0.11.2 RCurl_1.95-4.1 [36] Rsamtools_1.16.1 scales_0.2.4 sendmailR_1.1-2 splines_3.1.1 stats4_3.1.1 [41] stringr_0.6.2 survival_2.37-7 tools_3.1.1 VariantAnnotation_1.10.5 XML_3.98-1.1 [46] XVector_0.4.0 zlibbioc_1.10.0 Could someone please help me figure out how to generate these graphics? Thank you very much!! Best, Julia [[alternative HTML version deleted]]
cummeRbund cummeRbund • 2.4k views
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Loyal Goff ▴ 140
@loyal-goff-4989
Last seen 10.2 years ago
Hi Julia, In your scripts, you appear to be placing the created plot objects into a variable and not actually rendering them. Please try the following: > pdf("dispersion.pdf") > disp<-dispersionPlot(genes(cuff_data)) disp > dev.off() Note the direct use of 'disp' prior to closing the PDF device. This will call the default plot() method on the disp object and render it to your current device. Cheers, Loyal ------------------ Loyal A. Goff Postdoctoral Fellow CSAIL, MIT & SCRB, Harvard > On Jul 25, 2014, at 3:16 PM, "Sabet, Julia A" <julia.sabet@tufts.edu> wrote: > > Hello all, > I have been trying to use cummeRbund for a long time but I have not been able to get the graphics (plots) to show up either by "windows()" or by making a pdf file. I am using R on windows. I am pretty new to R so I am not sure if this is a general R issue or some issue specific to this package. I have been able to generate plots in other packages... This is the code that I used: > >> install.packages("RSQLite") >> install.packages("ggplot2") >> install.packages("reshape2") >> install.packages("plyr") >> install.packages("fastcluster") >> source("http://bioconductor.org/biocLite.R") >> biocLite("rtracklayer") >> biocLite("Gviz") >> biocLite("cummeRbund") >> setwd("C:/Users/jtoman01/Desktop/RNA Seq/combinedsexcuffdiff7.24") >> cuff_data <- readCufflinks() >> annot <- read.table("gene_exp.diff",sep="\t",header=T,na.string="-") >> addFeatures(cuff_data,annot,level="genes") >> windows() >> disp<-dispersionPlot(genes(cuff_data)) >> pdf("dispersion.pdf") >> disp<-dispersionPlot(genes(cuff_data)) >> dev.off() > > As far as warnings or errors, this was the only thing, which showed up after "cuff_data <- readCufflinks()": > Warning messages: > 1: attributes are not identical across measure variables; they will be dropped > 2: attributes are not identical across measure variables; they will be dropped > 3: attributes are not identical across measure variables; they will be dropped > 4: attributes are not identical across measure variables; they will be dropped > 5: attributes are not identical across measure variables; they will be dropped > 6: attributes are not identical across measure variables; they will be dropped > 7: attributes are not identical across measure variables; they will be dropped > 8: attributes are not identical across measure variables; they will be dropped > > Here is my sessionInfo(): > R version 3.1.1 (2014-07-10) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C LC_TIME=English_United States.1252 > > attached base packages: > [1] grid parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] cummeRbund_2.6.1 Gviz_1.8.4 rtracklayer_1.24.2 GenomicRanges_1.16.3 GenomeInfoDb_1.0.2 IRanges_1.22.9 > [7] BiocGenerics_0.10.0 fastcluster_1.1.13 plyr_1.8.1 reshape2_1.4 ggplot2_1.0.0 RSQLite_0.11.4 > [13] DBI_0.2-7 BiocInstaller_1.14.2 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.26.0 BatchJobs_1.3 BBmisc_1.7 Biobase_2.24.0 BiocParallel_0.6.1 > [6] biomaRt_2.20.0 Biostrings_2.32.1 biovizBase_1.12.1 bitops_1.0-6 brew_1.0-6 > [11] BSgenome_1.32.0 checkmate_1.2 cluster_1.15.2 codetools_0.2-8 colorspace_1.2-4 > [16] dichromat_2.0-0 digest_0.6.4 fail_1.2 foreach_1.4.2 Formula_1.1-2 > [21] GenomicAlignments_1.0.3 GenomicFeatures_1.16.2 gtable_0.1.2 Hmisc_3.14-4 iterators_1.0.7 > [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-33 matrixStats_0.10.0 munsell_0.4.2 > [31] proto_0.3-10 R.methodsS3_1.6.1 RColorBrewer_1.0-5 Rcpp_0.11.2 RCurl_1.95-4.1 > [36] Rsamtools_1.16.1 scales_0.2.4 sendmailR_1.1-2 splines_3.1.1 stats4_3.1.1 > [41] stringr_0.6.2 survival_2.37-7 tools_3.1.1 VariantAnnotation_1.10.5 XML_3.98-1.1 > [46] XVector_0.4.0 zlibbioc_1.10.0 > > Could someone please help me figure out how to generate these graphics? > Thank you very much!! > Best, > Julia > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
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Yay thank you so much!! ☺ From: Loyal A. Goff [mailto:lgoff@csail.mit.edu] Sent: Friday, July 25, 2014 3:33 PM To: Sabet, Julia A Cc: bioconductor@r-project.org Subject: Re: [BioC] cummeRbund graphics not working Hi Julia, In your scripts, you appear to be placing the created plot objects into a variable and not actually rendering them. Please try the following: pdf("dispersion.pdf") disp<-dispersionPlot(genes(cuff_data)) disp dev.off() Note the direct use of 'disp' prior to closing the PDF device. This will call the default plot() method on the disp object and render it to your current device. Cheers, Loyal ------------------ Loyal A. Goff Postdoctoral Fellow CSAIL, MIT & SCRB, Harvard On Jul 25, 2014, at 3:16 PM, "Sabet, Julia A" <julia.sabet@tufts.edu<mailto:julia.sabet@tufts.edu>> wrote: Hello all, I have been trying to use cummeRbund for a long time but I have not been able to get the graphics (plots) to show up either by "windows()" or by making a pdf file. I am using R on windows. I am pretty new to R so I am not sure if this is a general R issue or some issue specific to this package. I have been able to generate plots in other packages... This is the code that I used: install.packages("RSQLite") install.packages("ggplot2") install.packages("reshape2") install.packages("plyr") install.packages("fastcluster") source("http://bioconductor.org/biocLite.R") biocLite("rtracklayer") biocLite("Gviz") biocLite("cummeRbund") setwd("C:/Users/jtoman01/Desktop/RNA Seq/combinedsexcuffdiff7.24") cuff_data <- readCufflinks() annot <- read.table("gene_exp.diff",sep="\t",header=T,na.string="-") addFeatures(cuff_data,annot,level="genes") windows() disp<-dispersionPlot(genes(cuff_data)) pdf("dispersion.pdf") disp<-dispersionPlot(genes(cuff_data)) dev.off() As far as warnings or errors, this was the only thing, which showed up after "cuff_data <- readCufflinks()": Warning messages: 1: attributes are not identical across measure variables; they will be dropped 2: attributes are not identical across measure variables; they will be dropped 3: attributes are not identical across measure variables; they will be dropped 4: attributes are not identical across measure variables; they will be dropped 5: attributes are not identical across measure variables; they will be dropped 6: attributes are not identical across measure variables; they will be dropped 7: attributes are not identical across measure variables; they will be dropped 8: attributes are not identical across measure variables; they will be dropped Here is my sessionInfo(): R version 3.1.1 (2014-07-10) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] grid parallel stats graphics grDevices utils datasets methods base other attached packages: [1] cummeRbund_2.6.1 Gviz_1.8.4 rtracklayer_1.24.2 GenomicRanges_1.16.3 GenomeInfoDb_1.0.2 IRanges_1.22.9 [7] BiocGenerics_0.10.0 fastcluster_1.1.13 plyr_1.8.1 reshape2_1.4 ggplot2_1.0.0 RSQLite_0.11.4 [13] DBI_0.2-7 BiocInstaller_1.14.2 loaded via a namespace (and not attached): [1] AnnotationDbi_1.26.0 BatchJobs_1.3 BBmisc_1.7 Biobase_2.24.0 BiocParallel_0.6.1 [6] biomaRt_2.20.0 Biostrings_2.32.1 biovizBase_1.12.1 bitops_1.0-6 brew_1.0-6 [11] BSgenome_1.32.0 checkmate_1.2 cluster_1.15.2 codetools_0.2-8 colorspace_1.2-4 [16] dichromat_2.0-0 digest_0.6.4 fail_1.2 foreach_1.4.2 Formula_1.1-2 [21] GenomicAlignments_1.0.3 GenomicFeatures_1.16.2 gtable_0.1.2 Hmisc_3.14-4 iterators_1.0.7 [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-33 matrixStats_0.10.0 munsell_0.4.2 [31] proto_0.3-10 R.methodsS3_1.6.1 RColorBrewer_1.0-5 Rcpp_0.11.2 RCurl_1.95-4.1 [36] Rsamtools_1.16.1 scales_0.2.4 sendmailR_1.1-2 splines_3.1.1 stats4_3.1.1 [41] stringr_0.6.2 survival_2.37-7 tools_3.1.1 VariantAnnotation_1.10.5 XML_3.98-1.1 [46] XVector_0.4.0 zlibbioc_1.10.0 Could someone please help me figure out how to generate these graphics? Thank you very much!! Best, Julia [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto:bioconductor@r-project.org> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
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