I would like to plot the count of spliced reads supporting the junction above the splice bezier-curve, similar to the original sashimi plot now integrated in IGV.
Is there an option in Gviz for this?
You can set the parameter sashimiNumbers to TRUE. Then it should work. Either when you create the track or when using plotTracks function.
is it possible to store in a file the count of spliced reads displayed by the sashimi plot when i set the parameter sashimiNumbers to TRUE ?
To get those numbers via Gviz seems to me too complicated. You can use package GenomicAlignments to get those numbers from BAM files directly: function readGAlignments or readGAlignmentPairs to read in the data from BAM file and summarizeJunctions to produce the counts for junctions.
ok thank you so much for this help.