Draw breakpoints with coordinates given by posA, posB. Add additional layers for additional datasets as required.
This stage has expanded discussion of modifying of workflow, which is applicable for other drawing stages. See Development Notes for additional details.
The Breakpoint Panel (the upper right panel in BPS Structure plot), illustrates positions of breakpoints on an X,Y plane. For the TCGA_Virus workflow, the steps are,
- Draw Pindel predictions. Create GGP file with regions (rectangles) corresponding to Pindel RP predictions
- Draw Discordant predictions. Draw a point corresponding to location of discordant read.
- Draw Contig predictions Draw a + symbol corresponding to Contig prediction.
Steps 2 and 3 read in GGP file generated by the previous step, add a layer visualizing the data being plotted and save the new GGP file. Additional tools can be added here in an analogous way.
plot.ggp = ggplot() + geom_rect( pindel.data )
saveRDS()
followed by
plot.ggp = readRDS() + geom_point ( discordant.data )
saveRDS()
We create dat/GGP as a soft link (ln -s) to the output directory of the most recent GGP step
as a convenience for downstream stages.
By definition, here chrom A and B correspond to X and Y axes, resp. Also by
definition of BPC/BPR data, chrom a < chrom b. By default, chrom a = chrom A
and chrom b = chrom B, but this can be changed with FLIP_AB parameter defined
in ../bps.config. This allows control chrom/virus axes.