Gviz: Is it possible to plot coding (thick boxes) and non-coding (thin boxes) regions for an UcscTrack?
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@angelaheck-11271
Last seen 5.1 years ago

Hi!

 

  1.  I'm trying to plot coding and non-coding regions via the thinBoxFeature for an UCSC track. So far, I have downloaded the corresponding UCSC Track:

refGenes <- UcscTrack(genome = "hg19", chromosome = "chr1", track = "refGene", from=193028552, to=193060906, trackType = "GeneRegionTrack", rstarts = "exonStarts", rends = "exonEnds", gene = "name", symbol = "name", transcript = "name", strand = "strand", fill = "#8282d2", name = "refGene")


​However, I have not found a solution to define a feature for the download. I have tried the same with downloading a Biomart Track, and that worked:

 

biomTrack <- BiomartGeneRegionTrack(genome = "hg19", chromosome = "chr1", start = 193019886, end = 193065000, name = "RefSeq") 

feature(biomTrack) [1] "utr5" "utr5" "protein_coding" "utr5" "protein_coding" "utr5" "utr5" [8] "utr5" "protein_coding" "utr5" "utr5" ... 

2. ​In my plot the genes should have two names: the RefSeq gene Symbol (name2) and the UCSC name (name). Is there a smart way to define the names, other than downloading two tables/tracks ("refGene" and "knownGene") and combine them afterwards? 

Thank you in advance, Angela 


sessionInfo() 
R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin13.4.0 (64-bit) 
Running under: OS X 10.10.3 (Yosemite) 
locale: [1] de_CH.UTF-8/de_CH.UTF-8/de_CH.UTF-8/C/de_CH.UTF-8/de_CH.UTF-8 

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

other attached packages: [1] GenomicFeatures_1.24.5 AnnotationDbi_1.34.4 Biobase_2.32.0 rtracklayer_1.32.2 Gviz_1.16.1 [6] GenomicRanges_1.24.2 GenomeInfoDb_1.8.3 IRanges_2.6.1 S4Vectors_0.10.2 BiocGenerics_0.18.0 

loaded via a namespace (and not attached): [1] SummarizedExperiment_1.2.3 VariantAnnotation_1.18.5 splines_3.3.1 lattice_0.20-33 [5] colorspace_1.2-6 htmltools_0.3.5 chron_2.3-47 interactiveDisplayBase_1.10.3 [9] survival_2.39-5 XML_3.98-1.4 foreign_0.8-66 DBI_0.4-1 [13] ensembldb_1.4.7 BiocParallel_1.6.3 RColorBrewer_1.1-2 matrixStats_0.50.2 [17] plyr_1.8.4 zlibbioc_1.18.0 Biostrings_2.40.2 munsell_0.4.3 [21] gtable_0.2.0 latticeExtra_0.6-28 biomaRt_2.28.0 BiocInstaller_1.22.3 [25] httpuv_1.3.3 Rcpp_0.12.6 acepack_1.3-3.3 xtable_1.8-2 [29] BSgenome_1.40.1 scales_0.4.0 Hmisc_3.17-4 XVector_0.12.1 [33] mime_0.5 Rsamtools_1.24.0 gridExtra_2.2.1 AnnotationHub_2.4.2 [37] ggplot2_2.1.0 digest_0.6.9 biovizBase_1.20.0 shiny_0.13.2 [41] tools_3.3.1 bitops_1.0-6 RCurl_1.95-4.8 RSQLite_1.0.0 [45] dichromat_2.0-0 Formula_1.2-1 cluster_2.0.4 Matrix_1.2-6 [49] data.table_1.9.6 httr_1.2.1 R6_2.1.2 rpart_4.1-10 [53] GenomicAlignments_1.8.4 nnet_7.3-12
Gviz gene names thinBoxFeature UCSCtrack • 532 views
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