Hello,

The change Michael Lawrence made a few months ago on the tracks() to allow italics in the plot titles works well if you work with expression class objects, but I found an additional issue. I need to generate several plots and instead of writing each gene name manually, I would like to parse a variable to the italic function.

That means, instead of generating the plot title like this:

plot_title <- expression(paste("Variation in ", italic("AAAA"), " gene")) , I would like to replace "AAAA" by the variable gene_name.

In order to do so, I need to use the bquote function like this:

plot_title <- bquote('Variation in'~italic(.(gene_name))~'gene')

This function returns a "call" class object. Whenever I generate the plot title this way, it works with the plot or autoplot function, but the tracks function does not recognize it, and it returns the following error:

Error in validObject(.Object) :  invalid class "Tracks" object: invalid object for slot "main" in class "Tracks": got class "call", should be or extend class "characterORexpressionORNULL"

Can the "call" class be added to the "main" argument of the tracks function?

R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                         
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods 
[9] base     

other attached packages:
[1] Homo.sapiens_1.3.1                      TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[3] org.Hs.eg.db_3.4.0                      GO.db_3.4.0                           
[5] OrganismDbi_1.16.0                      GenomicFeatures_1.26.2                
[7] AnnotationDbi_1.36.0                    Biobase_2.34.0                        
[9] biovizBase_1.22.0                       ggbio_1.22.3                          
[11] ggplot2_2.2.0                           GenomicRanges_1.26.1                  
[13] GenomeInfoDb_1.10.2                     IRanges_2.8.1                         
[15] S4Vectors_0.12.1                        BiocGenerics_0.20.0                   
[17] RSQLite_1.1-1                          

loaded via a namespace (and not attached):
[1] httr_1.2.1                    AnnotationHub_2.6.4         
[3] splines_3.3.2                 Formula_1.2-1               
[5] shiny_0.14.2                  assertthat_0.1              
[7] interactiveDisplayBase_1.12.0 latticeExtra_0.6-28         
[9] RBGL_1.50.0                   BSgenome_1.42.0             
[11] Rsamtools_1.26.1              yaml_2.1.14                 
[13] lattice_0.20-34               digest_0.6.10               
[15] RColorBrewer_1.1-2            XVector_0.14.0              
[17] colorspace_1.3-2              htmltools_0.3.5             
[19] httpuv_1.3.3                  Matrix_1.2-7.1              
[21] plyr_1.8.4                    XML_3.98-1.5                
[23] biomaRt_2.30.0                zlibbioc_1.20.0             
[25] xtable_1.8-2                  scales_0.4.1                
[27] BiocParallel_1.8.1            htmlTable_1.7               
[29] tibble_1.2                    openssl_0.9.5               
[31] SummarizedExperiment_1.4.0    nnet_7.3-12                 
[33] lazyeval_0.2.0                survival_2.40-1             
[35] magrittr_1.5                  mime_0.5                    
[37] memoise_1.0.0                 GGally_1.3.0                
[39] foreign_0.8-67                graph_1.52.0                
[41] BiocInstaller_1.24.0          tools_3.3.2                 
[43] data.table_1.10.0             stringr_1.1.0               
[45] munsell_0.4.3                 cluster_2.0.5               
[47] ensembldb_1.6.2               Biostrings_2.42.1           
[49] base64_2.0                    grid_3.3.2                  
[51] RCurl_1.95-4.8                dichromat_2.0-0             
[53] VariantAnnotation_1.20.2      labeling_0.3                
[55] bitops_1.0-6                  gtable_0.2.0                
[57] DBI_0.5-1                     reshape_0.8.6               
[59] reshape2_1.4.2                R6_2.2.0                    
[61] GenomicAlignments_1.10.0      gridExtra_2.2.1             
[63] knitr_1.15.1                  rtracklayer_1.34.1          
[65] Hmisc_4.0-1                   stringi_1.1.2               
[67] Rcpp_0.12.8                   rpart_4.1-10                
[69] acepack_1.4.1   

Thank you very much,

Best,

Oswaldo

For now, I think you could just put the call object in an expression, i.e., expression(bquote(...)). I'll look into making it more user friendly.