I've just started using gviz - it looks really useful. Thanks for the package!
I'm plotting annotations and coverage (from a bam file) and am having trouble to get the labels to show up properly for the coverage tracks. Here's a very simple example that should show what I mean: in this example, I'd love to see the full label for the alignments track, and to have the labels for the two tracks left-aligned with each other.
Is there a way to control those things? I've been looking at the parameters for the track objects, but can't see anything that looks like what I need
thanks very much,
library(Gviz) afrom <- 2960000 ato <- 3160000 gtrack2 <- GenomeAxisTrack() fakeRegions <- GRanges(seqnames=rep("chr12",3), ranges=IRanges(start=c( 2970000, 3000000, 3050000), width=2000)) atrack <- AnnotationTrack(fakeRegions, name = "temp", rotation.title=0) alTrack <- AlignmentsTrack(system.file(package = "Gviz", "extdata", "gapped.bam"), isPaired = TRUE, rotation.title=0, type="coverage") plotTracks(c(gtrack2,atrack, alTrack), from = afrom, to = ato, chromosome = "chr12", title.width=6, sizes=c(1,1,1) ) sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.6 (El Capitan) locale:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  grid parallel stats4 stats graphics grDevices utils datasets methods base other attached packages:  Gviz_1.16.1 GenomicRanges_1.24.2 GenomeInfoDb_1.8.3 IRanges_2.6.1 S4Vectors_0.10.2  BiocGenerics_0.18.0 loaded via a namespace (and not attached):  SummarizedExperiment_1.2.3 VariantAnnotation_1.18.6 splines_3.3.1 lattice_0.20-33  colorspace_1.2-6 htmltools_0.3.5 rtracklayer_1.32.2 GenomicFeatures_1.24.5  chron_2.3-47 interactiveDisplayBase_1.10.3 survival_2.39-5 XML_3.98-1.4  foreign_0.8-66 DBI_0.4-1 ensembldb_1.4.7 BiocParallel_1.6.3  RColorBrewer_1.1-2 matrixStats_0.50.2 plyr_1.8.4 zlibbioc_1.18.0  Biostrings_2.40.2 munsell_0.4.3 gtable_0.2.0 latticeExtra_0.6-28  Biobase_2.32.0 biomaRt_2.28.0 BiocInstaller_1.22.3 httpuv_1.3.3  AnnotationDbi_1.34.4 Rcpp_0.12.6 acepack_1.3-3.3 xtable_1.8-2  BSgenome_1.40.1 scales_0.4.0 Hmisc_3.17-4 XVector_0.12.1  mime_0.5 Rsamtools_1.24.0 gridExtra_2.2.1 AnnotationHub_2.4.2  ggplot2_2.1.0 digest_0.6.9 biovizBase_1.20.0 shiny_0.13.2  tools_3.3.1 bitops_1.0-6 RCurl_1.95-4.8 RSQLite_1.0.0  dichromat_2.0-0 Formula_1.2-1 cluster_2.0.4 Matrix_1.2-6  data.table_1.9.6 httr_1.2.1 R6_2.1.2 rpart_4.1-10  GenomicAlignments_1.8.4 nnet_7.3-12