Hello, I'm trying to plot two Genomic ranges as Annotation Tracks (regs and rl14regionsR) in the same plot using Gviz along with an IdeogramTrack for chromosome 14 under hg38 with the following code:
gen<-"hg38"
chr="chr14"
atrack<-AnnotationTrack(regs, name= paste0("All expressed regions in ",names(files[j])))
grtrack <- AnnotationTrack(rl14regionsR, name = "Regions IGH", transcriptAnnotation = "symbol", background.title = "brown")
gtrack <- GenomeAxisTrack(chromosome = chr, genome = gen)
ideoTrack <- IdeogramTrack(genome = gen, chromosome = chr)
plotTracks(list(ideoTrack,grtrack,atrack), from= min(start(ranges(rl14))), to=max(end(ranges(rl14))))
Output:
As you can see atrack is not shown (only the indication of it). I get the following warning:
Warning messages:
1: In plotTracks(list(grtrack, atrack), from = min(start(ranges(rl14))), :
The track chromosomes in 'trackList' differ. Setting all tracks to chromosome 'chr14 '
If I try plotting only regs along with the Genome Axis track and the ideogram everything is shown correctly:
plotTracks(list(ideoTrack,gtrack, atrack), from= min(start(ranges(rl14))), to=max(end(ranges(rl14))))
But, when I do the same for rl14regionsR it doesn't work well and gives me once more the warning (either if I use chromosome="chr14") in the grtrack definition or not) and I don't get a clue of why if they come from the same chromosome in similar coordinates:
plotTracks(list(ideoTrack,gtrack, grtrack), from= min(start(ranges(rl14))), to=max(end(ranges(rl14))))
If I only plot the Genome axis track with grtrack (rl14regionsR) everything goes fine:
but if I I try plotting grtrack and rtrack together I still get the warning (and no rl14regionsR plot) even if I don't include any genome axis track or ideogram.
I've tried to use atrack as a GeneRegionTrack instead of an Annotation track unsuccessfully. I've also tried to use options(ucscChromosomeNames=FALSE) as suggested in IdeogramTrack from Gviz with chromosome name "4" rather "chr4" to see if the chromosome annotation was the problem but that didn't help either. I've already checked the vignette as suggested in gviz library plot 2 gene loci in the same figure, but I don't seem to find the correct way to use it.
rl14 is:
> rl14
GRanges object with 1 range and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr14 [105586437, 106879844] *
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
regs is:
regs
GRanges object with 1015 ranges and 6 metadata columns:
seqnames ranges strand | value area indexStart
<Rle> <IRanges> <Rle> | <numeric> <numeric> <integer>
up chr14 [105586708, 105586757] * | 1 50 1
up chr14 [105586809, 105586859] * | 1 51 51
up chr14 [105586869, 105586951] * | 1 83 102
up chr14 [105587004, 105587090] * | 1 87 185
up chr14 [105587125, 105587331] * | 1 207 272
.. ... ... ... . ... ... ...
up chr14 [106864234, 106864283] * | 1 50 112703
up chr14 [106872807, 106872827] * | 1 21 112753
up chr14 [106872903, 106872923] * | 1 21 112774
up chr14 [106874511, 106874560] * | 1 50 112795
up chr14 [106874650, 106874729] * | 1 80 112845
indexEnd cluster clusterL
<integer> <Rle> <Rle>
up 50 1 3435
up 101 1 3435
up 184 1 3435
up 271 1 3435
up 478 1 3435
.. ... ... ...
up 112752 339 50
up 112773 340 117
up 112794 340 117
up 112844 341 219
up 112924 341 219
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
rl14regionsR is:
> rl14regionsR
GRanges object with 33 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
1 chr14 [105586937, 105588394] *
28 chr14 [105588398, 105590398] *
29 chr14 [105591670, 105595520] *
2 chr14 [105600066, 105601727] *
26 chr14 [105600730, 105603080] *
.. ... ... ...
11 chr14 [105854343, 105856217] *
13 chr14 [105856219, 105857069] *
14 chr14 [105860305, 105863150] *
33 chr14 [105861950, 105862211] *
12 chr14 [105863196, 105863260] *
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=es_MX.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=es_MX.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=es_MX.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=es_MX.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid tools parallel stats4 stats graphics grDevices
[8] utils datasets methods base
other attached packages:
[1] EnsDb.Hsapiens.v79_2.99.0
[2] ensembldb_2.1.11
[3] AnnotationFilter_1.1.3
[4] Gviz_1.21.1
[5] TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0
[6] GenomicFeatures_1.29.8
[7] AnnotationDbi_1.39.2
[8] bumphunter_1.17.2
[9] locfit_1.5-9.1
[10] iterators_1.0.8
[11] foreach_1.4.3
[12] DESeq2_1.17.13
[13] AnnotationHub_2.9.9
[14] BiocParallel_1.11.6
[15] derfinderPlot_1.11.1
[16] rtracklayer_1.37.3
[17] tm_0.7-1
[18] NLP_0.1-11
[19] stringr_1.2.0
[20] getopt_1.20.0
[21] SRAdb_1.35.0
[22] RCurl_1.95-4.8
[23] bitops_1.0-6
[24] graph_1.55.0
[25] RSQLite_2.0
[26] xtable_1.8-2
[27] derfinder_1.11.6
[28] recount_1.3.4
[29] SummarizedExperiment_1.7.5
[30] DelayedArray_0.3.19
[31] matrixStats_0.52.2
[32] Biobase_2.37.2
[33] GenomicRanges_1.29.12
[34] GenomeInfoDb_1.13.4
[35] IRanges_2.11.12
[36] S4Vectors_0.15.5
[37] BiocGenerics_0.23.0
[38] BiocInstaller_1.27.3
loaded via a namespace (and not attached):
[1] colorspace_1.3-2 biovizBase_1.25.1
[3] qvalue_2.9.0 htmlTable_1.9
[5] XVector_0.17.0 base64enc_0.1-3
[7] dichromat_2.0-0 bit64_0.9-7
[9] interactiveDisplayBase_1.15.0 codetools_0.2-15
[11] splines_3.4.1 ggbio_1.25.3
[13] geneplotter_1.55.0 knitr_1.17
[15] Formula_1.2-2 jsonlite_1.5
[17] Rsamtools_1.29.0 annotate_1.55.0
[19] cluster_2.0.6 shiny_1.0.4
[21] rentrez_1.1.0 compiler_3.4.1
[23] httr_1.3.0 backports_1.1.0
[25] assertthat_0.2.0 Matrix_1.2-11
[27] lazyeval_0.2.0 limma_3.33.7
[29] acepack_1.4.1 htmltools_0.3.6
[31] prettyunits_1.0.2 gtable_0.2.0
[33] GenomeInfoDbData_0.99.1 reshape2_1.4.2
[35] doRNG_1.6.6 Rcpp_0.12.12
[37] slam_0.1-40 Biostrings_2.45.3
[39] mime_0.5 rngtools_1.2.4
[41] XML_3.98-1.9 zlibbioc_1.23.0
[43] scales_0.4.1 BSgenome_1.45.1
[45] VariantAnnotation_1.23.8 ProtGenerics_1.9.0
[47] RBGL_1.53.0 GEOquery_2.43.0
[49] derfinderHelper_1.11.1 RColorBrewer_1.1-2
[51] yaml_2.1.14 curl_2.8.1
[53] memoise_1.1.0 gridExtra_2.2.1
[55] ggplot2_2.2.1 downloader_0.4
[57] pkgmaker_0.22 biomaRt_2.33.4
[59] rpart_4.1-11 reshape_0.8.7
[61] latticeExtra_0.6-28 stringi_1.1.5
[63] genefilter_1.59.0 checkmate_1.8.3
[65] pkgconfig_2.0.1 rlang_0.1.2
[67] GenomicFiles_1.13.10 lattice_0.20-35
[69] GenomicAlignments_1.13.5 htmlwidgets_0.9
[71] bit_1.1-12 GGally_1.3.2
[73] plyr_1.8.4 magrittr_1.5
[75] R6_2.2.2 Hmisc_4.0-3
[77] DBI_0.7 foreign_0.8-69
[79] survival_2.41-3 nnet_7.3-12
[81] tibble_1.3.3 OrganismDbi_1.19.0
[83] progress_1.1.2 data.table_1.10.4
[85] blob_1.1.0 digest_0.6.12
[87] httpuv_1.3.5 munsell_0.4.3
[89] registry_0.3
