Gviz, DataTrack, Group plotting
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Last seen 9.6 years ago
Hi. First of all thanks for this great package. I already made some nice figures with it. However, now I would like to plot from a GRanges objects (actually with the group option), which unfortunately fails. When following the vignitte instructions 4.3 DataTrack I experience the following errors: #first data(twoGroups) #when I instantiate a DataTrack object: dTrack<- DataTrack(twoGroups,name="Uniform") #I got this error:Error in DataTrack(twoGroups, name = "Uniform") : #A chromosome must be specified for this annotation track. #so I add a chromosome, which works fine... dTrack<- DataTrack(twoGroups,chromosome="chrX",name="Uniform") #the next error occurs when I try to plot the track: plotTracks(dTrack) #Error in .defaultRange(trackList, from = from, to = to, extend.left = extend.left, : #Unable to determine plotting ranges from the supplied track(s) dTrack<-DataTrack(twoGroups,chromosome="chrX",name="Uniform",ranges=tw oGroups) plotTracks(dTrack) #Error in .local(x, i, j, ...) : (subscript) logical subscript too long Does anyone have similar problems or knows how to solve this? Thanks in advance, Jonas -- output of sessionInfo(): R version 2.15.1 (2012-06-22) Platform: x86_64-pc-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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] splines grid stats graphics grDevices utils datasets [8] methods base other attached packages: [1] ShortRead_1.14.4 latticeExtra_0.6-19 RColorBrewer_1.0-5 [4] Rsamtools_1.8.5 Biostrings_2.24.1 GenomicRanges_1.8.9 [7] IRanges_1.14.4 BiocGenerics_0.2.0 GenomeGraphs_1.16.0 [10] biomaRt_2.12.0 snpStats_1.6.0 Matrix_1.0-6 [13] lattice_0.20-6 survival_2.36-14 Gviz_1.0.1 loaded via a namespace (and not attached): [1] AnnotationDbi_1.18.1 Biobase_2.16.0 bitops_1.0-4.1 [4] BSgenome_1.24.0 DBI_0.2-5 hwriter_1.3 [7] RCurl_1.91-1 RSQLite_0.11.1 rtracklayer_1.16.3 [10] stats4_2.15.1 tools_2.15.1 XML_3.9-4 [13] zlibbioc_1.2.0 -- Sent via the guest posting facility at bioconductor.org.
Annotation Annotation • 2.0k views
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