I'm trying to make a gene model plot using the ggbio tracks function. When I do autoplot alone, it looks fine, but when I use tracks, the x-axis ticks are misaligned. Please see if you can reproduce the issue using the code below:
library(ggbio)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
data(genesymbol, package = "biovizBase")
wh <- genesymbol[c("BRCA1", "NBR1")]
wh <- range(wh, ignore.strand = TRUE)
p <- autoplot(txdb, which=wh)
# Plot 1: http://www.stanford.edu/~cooketho/test1.png
p
# Plot 2: http://www.stanford.edu/~cooketho/test2.png
tracks(p, p)
sessionInfo()
R version 3.1.2 (2014-10-31)
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=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] XVector_0.6.0
[2] TxDb.Hsapiens.UCSC.hg19.knownGene_3.0.0
[3] GenomicFeatures_1.18.3
[4] AnnotationDbi_1.28.1
[5] Biobase_2.26.0
[6] GenomicRanges_1.18.4
[7] GenomeInfoDb_1.2.4
[8] IRanges_2.0.1
[9] S4Vectors_0.4.0
[10] ggbio_1.14.0
[11] ggplot2_1.0.0
[12] BiocGenerics_0.12.1
loaded via a namespace (and not attached):
[1] acepack_1.3-3.3 base64enc_0.1-2 BatchJobs_1.5
[4] BBmisc_1.8 BiocParallel_1.0.1 biomaRt_2.22.0
[7] Biostrings_2.34.1 biovizBase_1.14.1 bitops_1.0-6
[10] brew_1.0-6 BSgenome_1.34.1 checkmate_1.5.1
[13] cluster_1.15.3 codetools_0.2-10 colorspace_1.2-4
[16] DBI_0.3.1 dichromat_2.0-0 digest_0.6.8
[19] fail_1.2 foreach_1.4.2 foreign_0.8-62
[22] Formula_1.2-0 GenomicAlignments_1.2.1 GGally_0.5.0
[25] graph_1.44.1 grid_3.1.2 gridExtra_0.9.1
[28] gtable_0.1.2 Hmisc_3.14-6 iterators_1.0.7
[31] labeling_0.3 lattice_0.20-29 latticeExtra_0.6-26
[34] MASS_7.3-37 munsell_0.4.2 nnet_7.3-8
[37] OrganismDbi_1.8.0 plyr_1.8.1 proto_0.3-10
[40] RBGL_1.42.0 RColorBrewer_1.1-2 Rcpp_0.11.4
[43] RCurl_1.95-4.5 reshape_0.8.5 reshape2_1.4.1
[46] rpart_4.1-8 Rsamtools_1.18.2 RSQLite_1.0.0
[49] rtracklayer_1.26.2 scales_0.2.4 sendmailR_1.2-1
[52] splines_3.1.2 stringr_0.6.2 survival_2.37-7
[55] tools_3.1.2 VariantAnnotation_1.12.9 XML_3.98-1.1
[58] zlibbioc_1.12.0
I also tried the developmental version, and had the same problem (see package info below):
> sessionInfo()
R Under development (unstable) (2015-02-03 r67717)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.4 LTS)
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=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.0.0
[2] GenomicFeatures_1.19.18
[3] AnnotationDbi_1.29.17
[4] Biobase_2.27.1
[5] GenomicRanges_1.19.35
[6] GenomeInfoDb_1.3.12
[7] BiocInstaller_1.17.5
[8] XVector_0.7.3
[9] IRanges_2.1.36
[10] S4Vectors_0.5.17
[11] ggbio_1.15.1
[12] ggplot2_1.0.0
[13] BiocGenerics_0.13.4
loaded via a namespace (and not attached):
[1] Rcpp_0.11.4 biovizBase_1.15.2
[3] lattice_0.20-29 Rsamtools_1.19.26
[5] Biostrings_2.35.7 digest_0.6.8
[7] foreach_1.4.2 plyr_1.8.1
[9] BatchJobs_1.5 acepack_1.3-3.3
[11] RSQLite_1.0.0 zlibbioc_1.13.0
[13] rpart_4.1-8 checkmate_1.5.1
[15] labeling_0.3 proto_0.3-10
[17] splines_3.2.0 BiocParallel_1.1.13
[19] stringr_0.6.2 foreign_0.8-62
[21] RCurl_1.95-4.5 biomaRt_2.23.5
[23] munsell_0.4.2 sendmailR_1.2-1
[25] rtracklayer_1.27.7 base64enc_0.1-2
[27] BBmisc_1.9 nnet_7.3-8
[29] fail_1.2 gridExtra_0.9.1
[31] Hmisc_3.14-6 codetools_0.2-10
[33] XML_3.98-1.1 reshape_0.8.5
[35] GenomicAlignments_1.3.27 MASS_7.3-38
[37] bitops_1.0-6 grid_3.2.0
[39] RBGL_1.43.0 GGally_0.5.0
[41] gtable_0.1.2 DBI_0.3.1
[43] scales_0.2.4 graph_1.45.1
[45] reshape2_1.4.1 latticeExtra_0.6-26
[47] brew_1.0-6 Formula_1.2-0
[49] RColorBrewer_1.1-2 iterators_1.0.7
[51] tools_3.2.0 dichromat_2.0-0
[53] BSgenome_1.35.16 OrganismDbi_1.9.3
[55] survival_2.37-7 colorspace_1.2-4
[57] cluster_2.0.1 VariantAnnotation_1.13.28
I do see the issue you are reporting but it took a bit of gawking to appreciate it.
It seems that the data space was rescaled to cope with the additional vertical content but
the bounding geometry was not updated. Please contact the maintainer, your example is very clear.