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
Dear Michael Lawrence,
This was my first guess, that turning the
bquote(...))into anexpression(bquote(..))object would work.The problem I get with this approach is that instead of getting the real gene name into the output plot title, I get the following character string:
"bquote(Variation in .(gene_name) gene)"
That was the reason to ask you to include the call object into the accepted formats for the main class of the tracks function.
Thank you very much for your time,
Best,
Oswaldo
Sorry, I meant
as.expression(bquote(...)).Thank you,
That was my fault. I wasn't converting the bquote function into an expression in the right way.
This will work for me like this.
Best,
Oswaldo