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I'm trying to plot specific transcripts from a gene using Gviz and I'm retrieving this information from UCSC using the function UcscTrack. However, because there are longer transcripts in the same region of interest, Gviz is plotting all the transcripts that overlap this region, extending the start and end of my plot.
For example, I wanna plot chrX:31,135,000-31,287,000
a <- AnnotationTrack(start=31135000, end=31287000,chromosome="chrX", genome="hg19", name="AnnotationTrack") gtrack <- GenomeAxisTrack() itrack <- IdeogramTrack(genome = "hg19", chromosome = "chrX") knownGenes <- UcscTrack(genome = "hg19", chromosome = "chrX", track = "knownGene", from = 31135000, to = 31287000, trackType = "GeneRegionTrack", rstarts = "exonStarts", rends = "exonEnds", gene = "name", symbol = "name", transcript = "name", strand = "strand", fill = "#8282d2", name = "UCSC Genes") plotTracks(list(itrack,gtrack,knownGenes))
But, when I plot it, the region goes from 31,000,000 to 33,500,000.
Is there a way I can force Gviz to plot only my region of interest instead of extending it due to longer transcripts?