Re: Plotting arbitrary lines at Gviz plotTracks

Hi Vinicius,
It looks like you sample image got stripped, so I can¹t see what exactly
you are aiming for. That being said, from your description it seems like
you are asking for a feature that is not available in Gviz. There are no
low-level plotting functions at your disposal like in base R graphics.
With quite a bit of effort you could archive some of this by using the
CustomTrack class, but it would involve a bunch of steps that Gviz tries
to hide away from the user, like computing the optimal stacking of
overlaying genes, etc.
Florian 

On 26/08/14 08:44, "Vinicius Henrique da Silva"
<[email protected]> wrote:

>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]]
>
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