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Sabet, Julia A
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180
@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
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