[BioC] New error in Gviz
Miles Pufall
miles.pufall at gmail.com
Mon May 5 18:00:21 CEST 2014
Hi -
I've been making figures using BigWig files in Gviz without incident on a Linux machine and more recently on my Mac, but when I tried rerunning an existing script I got an error that I don't really understand. Below is my script and the output - it occurs during plotTracks, but involves unlist and split functions that I haven't specified. Is this a bug or have I failed to updat emy script for the newest version of Gviz?
Thx -
Miles
**********************Script
library("Gviz")
library(GenomicFeatures)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
setwd("/Volumes/PUFALL_2TB")
itrack <- IdeogramTrack(genome = "hg19", cex = 1.4)
gtrack <- GenomeAxisTrack(cex=1)
B1_dex<-DataTrack("B1_ChIPseq/B1_all_treat_pileup.bw",genome="hg19", cex.title=1.2, cex.axis=1, background.title="darkgray",
col.histogram="blue", fill.histogram="blue", name ="B1", ylim=c(0,3))
sup_dex<-DataTrack("SUP-B15/10min/sup_b15_10min_treat_pileup.bw",genome="hg19", cex.title=1.2, cex.axis=1,background.title="darkgray",
col.histogram="blue", fill.histogram="blue", name ="SUP-B15", ylim=c(0,3))
rch_dex<-DataTrack("RCH-ACV/rch_acv_treat_pileup.bw",genome="hg19", cex.title=1.2, cex.axis=1,background.title="darkgray",
col.histogram="blue", fill.histogram="blue", name ="RCH-ACV", ylim=c(0,3))
HM3101_dex<-DataTrack("HM3101/HM3101_dex_1uM_treat_pileup.bw",genome="hg19", cex.title=1.2, cex.axis=1,background.title="darkgray",
col.histogram="blue", fill.histogram="blue", name ="HM3101", ylim=c(0,3))
grtrack <- GeneRegionTrack(txdb, genome = "hg19",name="BCL6", stacking="pack",stackHeight = 0.4,geneSymbols=TRUE, cex=1, cex.title=1.5, background.title="darkgray",
chromosome = "chr3")
plotTracks(list(itrack,gtrack,grtrack,B1_dex,sup_dex,rch_dex,HM3101_dex),from=187437000, to=187470000,type="histogram",chromosome="chr3")
*************Output
R version 3.1.0 (2014-04-10) -- "Spring Dance"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin10.8.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library("Gviz")
Loading required package: grid
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport,
clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply,
parSapplyLB
The following object is masked from ‘package:stats’:
xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call,
duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply,
Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unlist
Loading required package: S4Vectors
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Warning messages:
1: multiple methods tables found for ‘compare’
2: multiple methods tables found for ‘seqinfo’
3: multiple methods tables found for ‘seqinfo<-’
4: multiple methods tables found for ‘seqnames’
5: multiple methods tables found for ‘seqinfo’
6: multiple methods tables found for ‘seqinfo<-’
7: multiple methods tables found for ‘seqnames’
8: multiple methods tables found for ‘mcols<-’
9: multiple methods tables found for ‘values’
10: multiple methods tables found for ‘values<-’
> library(GenomicFeatures)
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with 'browseVignettes()'. To cite
Bioconductor, see 'citation("Biobase")', and for packages
'citation("pkgname")'.
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
> setwd("/Volumes/PUFALL_2TB")
> itrack <- IdeogramTrack(genome = "hg19", cex = 1.4)
> gtrack <- GenomeAxisTrack(cex=1)
> B1_dex<-DataTrack("B1_ChIPseq/B1_all_treat_pileup.bw",genome="hg19", cex.title=1.2, cex.axis=1, background.title="darkgray",
+ col.histogram="blue", fill.histogram="blue", name ="B1", ylim=c(0,3))
>
> sup_dex<-DataTrack("SUP-B15/10min/sup_b15_10min_treat_pileup.bw",genome="hg19", cex.title=1.2, cex.axis=1,background.title="darkgray",
+ col.histogram="blue", fill.histogram="blue", name ="SUP-B15", ylim=c(0,3))
>
> rch_dex<-DataTrack("RCH-ACV/rch_acv_treat_pileup.bw",genome="hg19", cex.title=1.2, cex.axis=1,background.title="darkgray",
+ col.histogram="blue", fill.histogram="blue", name ="RCH-ACV", ylim=c(0,3))
>
> HM3101_dex<-DataTrack("HM3101/HM3101_dex_1uM_treat_pileup.bw",genome="hg19", cex.title=1.2, cex.axis=1,background.title="darkgray",
+ col.histogram="blue", fill.histogram="blue", name ="HM3101", ylim=c(0,3))
>
> grtrack <- GeneRegionTrack(txdb, genome = "hg19",name="BCL6", stacking="pack",stackHeight = 0.4,geneSymbols=TRUE, cex=1, cex.title=1.5, background.title="darkgray",
+ chromosome = "chr3")
>
> plotTracks(list(itrack,gtrack,grtrack,B1_dex,sup_dex,rch_dex,HM3101_dex),from=187437000, to=187470000,type="histogram",chromosome="chr3")
Error in unlist(range(split(ranges(x), group(x)))) :
error in evaluating the argument 'x' in selecting a method for function 'unlist': Error in split(ranges(x), group(x)) :
error in evaluating the argument 'f' in selecting a method for function 'split': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘values’ for signature ‘"GeneRegionTrack"’
>
****************sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 GenomicFeatures_1.17.4 AnnotationDbi_1.27.4
[4] Biobase_2.25.0 Gviz_1.9.1 GenomicRanges_1.17.12
[7] GenomeInfoDb_1.1.2 IRanges_1.99.12 S4Vectors_0.0.6
[10] BiocGenerics_0.11.1
loaded via a namespace (and not attached):
[1] BatchJobs_1.2 BBmisc_1.6 BiocParallel_0.7.0 biomaRt_2.21.0 Biostrings_2.33.5
[6] biovizBase_1.13.6 bitops_1.0-6 brew_1.0-6 BSgenome_1.33.2 cluster_1.15.2
[11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 digest_0.6.4
[16] fail_1.2 foreach_1.4.2 Formula_1.1-1 GenomicAlignments_1.1.7 Hmisc_3.14-4
[21] iterators_1.0.7 lattice_0.20-29 latticeExtra_0.6-26 matrixStats_0.8.14 munsell_0.4.2
[26] plyr_1.8.1 R.methodsS3_1.6.1 RColorBrewer_1.0-5 Rcpp_0.11.1 RCurl_1.95-4.1
[31] Rsamtools_1.17.9 RSQLite_0.11.4 rtracklayer_1.25.4 scales_0.2.4 sendmailR_1.1-2
[36] splines_3.1.0 stats4_3.1.0 stringr_0.6.2 survival_2.37-7 tools_3.1.0
[41] VariantAnnotation_1.11.3 XML_3.98-1.1 XVector_0.5.6 zlibbioc_1.11.1
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