Functions to plot copy number segments

[lbeltrame]

Currently you can plot either calls, or raw log2ratios. You can't, however, plot segments on top of the log2ratio raw data with the currently available functions.

[bernatgel]

CopyNumberPlots is based on karyoploteR and it inherits it's flexibility, so I'm convinced it would be possible to plot pretty much anything you'd need :) Can you post an example of what you're trying to accomplish? or a hand drawing or similar? I can try to help you with that

[lbeltrame]

I made a PoC by "tricking" the existing functions:

segment_bins = loadSNPData("bins.seg", chr.col="chr", start.col="start", end.col="end", lrr.col="logR", genome="hg38")

segment_cn = loadCopyNumberCallsSeg("calls.seg", chr.col="chr", start.col="start", end.col="end", segment.value.col="median", genome="hg38")

kp = plotKaryotype(plot.type=5, genome="hg38", chromosomes=c(paste0("chr", 1:22), "chrX"), cex=0.7)
plotLRR(kp, snps=segment_bins ymin=-2, ymax=2, labels="log2ratio", points.cex=0.4)
# Notice how I used the cn.column parameter below
plotCopyNumberCallsAsLines(kp, cn.calls=segment_cn style="segments", r=0, r1=1, cn.column="segment.value", ymin=-2, ymax=2, col="#fd0002", add.axis=F, labels=NA,lwd=4)

Which gives, with my data:

[bernatgel]

Hi @lbeltrame

I was going to suggest you to dom just what you did! So it's possible to create the plot with CopyNumberPlots. How else you'd have expected the system to work? A different function for the segments? (you can use directly karyoploteR::kpSegments so it'd feel less as tricking the functions)

[lbeltrame]

I actually had issues with kpSegments as it had issues in plotting with the same scale (but I guess I just messed up the paramters).

If you think this is the way to go, perhaps a mention in the documentation would suffice: these types of plots are quite used to see if segmentation is fine (and also for comparison purposes since karyotypeR is very flexible in this regard).

[bernatgel]

Ok! It might make sense to create a specific function for that. It could even compute the median
of each segment from the LRR values and the segmentation if needed.

If you keep having issues with kpSegments just ask :)