Dear all,

I would like to create a custom track for Gviz. I found the CustomTrack class but didn't get it working properly. Plotting only the CustomTrack works as expected however, when plotting a tracklist the CustomTrack appears twice on different vertical locations.

Does anyone have experience using Gviz CustomTrack?

Kind regards,

Maarten van Iterson

The following minimal example shows the issue:

library(Gviz)
cTrack <- CustomTrack(plottingFunction = function(GdObject, prepare) {grid.text("customtrack"); return(invisible(GdObject))})
plotTracks(cTrack,  from = 1, to = 100) ##only CustomTrack

gtrack <- GenomeAxisTrack()                          
plotTracks(c(cTrack, gtrack),  from = 1, to = 100) ##Plotting two tracks

sessionInfo()
R Under development (unstable) (2014-07-22 r66228)
Platform: x86_64-unknown-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] parallel  grid      stats     graphics  grDevices utils     datasets
[8] methods   base     

other attached packages:
[1] Gviz_1.9.13           GenomicRanges_1.17.34 GenomeInfoDb_1.1.18  
[4] IRanges_1.99.24       S4Vectors_0.1.2       BiocGenerics_0.11.4  

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3           AnnotationDbi_1.27.9     
 [3] BatchJobs_1.3             BBmisc_1.7               
 [5] Biobase_2.25.0            BiocParallel_0.99.10     
 [7] biomaRt_2.21.1            Biostrings_2.33.13       
 [9] biovizBase_1.13.9         bitops_1.0-6             
[11] brew_1.0-6                BSgenome_1.33.8          
[13] checkmate_1.4             cluster_1.14.4           
[15] codetools_0.2-8           colorspace_1.2-4         
[17] DBI_0.3.0                 dichromat_2.0-0          
[19] digest_0.6.4              fail_1.2                 
[21] foreach_1.4.2             foreign_0.8-57           
[23] Formula_1.1-2             GenomicAlignments_1.1.24
[25] GenomicFeatures_1.17.14   Hmisc_3.14-5             
[27] iterators_1.0.7           lattice_0.20-24          
[29] latticeExtra_0.6-26       matrixStats_0.10.0       
[31] munsell_0.4.2             nnet_7.3-7               
[33] plyr_1.8.1                R.methodsS3_1.6.1        
[35] RColorBrewer_1.0-5        Rcpp_0.11.2              
[37] RCurl_1.95-4.3            rpart_4.1-3              
[39] Rsamtools_1.17.32         RSQLite_0.11.4           
[41] rtracklayer_1.25.13       scales_0.2.4             
[43] sendmailR_1.1-2           splines_3.2.0            
[45] stats4_3.2.0              stringr_0.6.2            
[47] survival_2.37-7           tools_3.2.0              
[49] VariantAnnotation_1.11.24 XML_3.98-1.1             
[51] XVector_0.5.7             zlibbioc_1.11.1         

Hi Maarten,

try this:

library(Gviz)
cTrack <- CustomTrack(plottingFunction = function(GdObject, prepare) {if(!prepare) grid.text("customtrack"); return(invisible(GdObject))})

gtrack <- GenomeAxisTrack()                          
plotTracks(c(cTrack, gtrack),  from = 1, to = 100) ##Plotting two tracks

Essentially the idea of the prepare parameter is that Gviz track plotting functions are called twice. Once in prepare mode to set up parameters like stacks or font sizes, and then a second time to do the actual plotting. 

I should probably hide this fact from the user in CustomTracks by not calling the plotting function in the preparation phase, and definitely should work on the documentation.

Florian