Dear Florian,
I would like to show the common name of genetic elements and not the UCSC's identifier (I think it is what we see).
In addition, I would like to know if it is possible to have the color of genetic elements that depends on the type of its features as you did for Ensembl data via BiomartGeneRegionTrack.
Regards, Tiphaine
Currently, it is my code.
gen <- "hg19" chr <- "chr13" end <- 32507139 start <- 31264764 ucsc4 <- UcscTrack(genome = gen, chromosome = chr,track = "knownGene", from = start, to = end, trackType = "GeneRegionTrack", rstarts = "exonStarts", rends = "exonEnds", gene = "name", symbol = "name", transcript = "name", strand = "strand", id = "name", name = "UCSC Genes",stacking="pack", group="name", fontcolor="black", groupAnnotation = "group", just.group = "above",size=2, showId=TRUE, col.line = NULL, col = NULL) plotTracks(ucsc4)
sessionInfo() R version 3.1.2 (2014-10-31) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel grid stats graphics grDevices utils datasets methods [10] base other attached packages: [1] XVector_0.6.0 rtracklayer_1.26.2 BiocInstaller_1.16.1 coMET_0.99.8 [5] Gviz_1.10.9 GenomicRanges_1.18.4 GenomeInfoDb_1.2.4 IRanges_2.0.1 [9] S4Vectors_0.4.0 BiocGenerics_0.12.1 biomaRt_2.22.0