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Question: Plotting arbitrary lines at Gviz plotTracks
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gravatar for Vinicius Henrique da Silva
4.0 years ago by
Brazil
I would like to plot lines between two itens at different `AnnotationTrack`, or simple between two coordinates in my `Gviz`plot. genes data.frame: start end 72529373 72690449 75457896 75536848 76867833 76922959 75664651 75870596 76958977 77024110 72065147 72204484 74198711 74199129 74816044 74978179 76758753 76864805 77032585 77176916 73574461 73704802 library(Gviz) library(GenomicRanges) ideoTrack <- IdeogramTrack(genome = "bosTau6", chromosome = "chr12", fontsize=14, ucscChromosomeNames=TRUE) axisTrack <- GenomeAxisTrack(range = IRanges(start = c(71959908, 76756891), end = c(72409907, 77206892), names = rep("Neighborhood", 2)), fontsize=14, showId = TRUE, cex.id = 0.5, col.id = "black") aTgenes1 <- AnnotationTrack(genes, name = "Genes", genome ="bosTau6", chromosome ="chr12", showId = TRUE, stacking ="dense") aTgenes2 <- AnnotationTrack(genes, name = "Genes", genome ="bosTau6", chromosome ="chr12", showId = TRUE, stacking ="dense") plotTracks(list(ideoTrack, axisTrack, aTgenes1, aTgenes2), from = 71959908, to = 77206892, sizes=c(1,1,1,1), margin=40, littleTicks = TRUE)This above code result in this plot: Considering the 11 plotted genes (the fourth gene is very small and hard to see), I have the follow interaction between the genes: gene 1 -> gene 2 and gene 11 gene 3 -> gene 5 gene 7 -> gene 6 With this interaction I expect some final plot similar to this picture: I had tried some approachs that works in normal plots but not to Gviz plots. Some ideas? Thank you very much! Vinicius [[alternative HTML version deleted]]
ADD COMMENTlink written 4.0 years ago by Vinicius Henrique da Silva20
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