Hi, 

Gviz is amazing to visualize genomic data (big thanks to the developers).

I was wondering, it possible to plot the coverage in a log scale from an AlignmentTrack? I have been trying to do this by passing the parameter 'transformation' but I don't see any effect in the plot:

library(Gviz)
afrom <- 2960000
ato <- 3160000
alTrack <- AlignmentsTrack(system.file(package = "Gviz", "extdata", "gapped.bam"),
                           isPaired = TRUE)
bmt <- BiomartGeneRegionTrack(genome = "hg19", chromosome = "chr12",
                              start = afrom, end = ato,
                              filter = list(with_ox_refseq_mrna = TRUE),
                              stacking = "dense")
plotTracks(c(bmt, alTrack), from = afrom, to = ato,
           chromosome = "chr12", type="coverage",
           transformation=function(x){log2(x+1)})

Am I missing something?

Alejandro Reyes

ps. My sessionInfo()

> sessionInfo()
R Under development (unstable) (2016-05-09 r70593)
Platform: x86_64-apple-darwin15.3.0 (64-bit)
Running under: OS X 10.11.5 (El Capitan)

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] grid      parallel  stats4    stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
[1] Gviz_1.16.1           GenomicRanges_1.23.27 GenomeInfoDb_1.7.6   
[4] IRanges_2.5.46        S4Vectors_0.9.51      BiocGenerics_0.17.5  
[7] BiocInstaller_1.22.2 

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.1.24   VariantAnnotation_1.18.1     
 [3] splines_3.4.0                 lattice_0.20-33              
 [5] colorspace_1.2-6              htmltools_0.3.5              
 [7] rtracklayer_1.31.10           GenomicFeatures_1.23.30      
 [9] interactiveDisplayBase_1.10.3 survival_2.39-2              
[11] XML_3.98-1.4                  foreign_0.8-66               
[13] DBI_0.3.1                     ensembldb_1.4.6              
[15] BiocParallel_1.5.21           RColorBrewer_1.1-2           
[17] matrixStats_0.50.2            plyr_1.8.3                   
[19] zlibbioc_1.17.1               Biostrings_2.39.14           
[21] munsell_0.4.3                 gtable_0.2.0                 
[23] latticeExtra_0.6-28           Biobase_2.31.3               
[25] biomaRt_2.27.2                httpuv_1.3.3                 
[27] AnnotationDbi_1.33.12         Rcpp_0.12.4.5                
[29] acepack_1.3-3.3               xtable_1.8-2                 
[31] BSgenome_1.40.0               scales_0.4.0                 
[33] Hmisc_3.17-3                  XVector_0.11.8               
[35] mime_0.4                      Rsamtools_1.24.0             
[37] gridExtra_2.2.1               AnnotationHub_2.4.2          
[39] ggplot2_2.1.0                 digest_0.6.9                 
[41] biovizBase_1.20.0             shiny_0.13.2                 
[43] tools_3.4.0                   bitops_1.0-6                 
[45] RCurl_1.95-4.8                RSQLite_1.0.0                
[47] dichromat_2.0-0               Formula_1.2-1                
[49] cluster_2.0.4                 Matrix_1.2-5                 
[51] httr_1.1.0                    R6_2.1.2                     
[53] rpart_4.1-10                  GenomicAlignments_1.7.21     
[55] nnet_7.3-12                   compiler_3.4.0