It's been a few years and looks like there still isn't any option to disable smoothing for AlignmentsTrack
. At least I don't see any way to do it from the Gviz documentation and the the R source code in R/Gviz-methods.R
in the drawGD
method for AlignmentsTrack
still forces the smoothing logic pointed out by Florian's comment when the read size is more than 2 pixels.
As workaround, I use DataTrack
as explained in the section "Building DataTrack objects from files" section of the Gviz vignette copied here for convenience:
bamFile <- system.file("extdata/test.bam", package = "Gviz")
dTrack4 <- DataTrack(range = bamFile, genome = "hg19", type = "l",
name = "Coverage", window = -1,
chromosome = "chr1")
plotTracks(dTrack4, from = 189990000, to = 190000000)
... you don't get the benefit of the rug plot, fill color, etc. as you would with AlignmentsTrack
, nevertheless using DataTrack
seems practical for simple use cases of plotting coverage.
I have sparse reads, and use the type = "h"
to get a histogram similar to the UCSC browser.
Dear Florian,
I did just as you said and something is inconsistent here...
I select the maximum coverage as:
And it prints 352; gr holds the interesting genomic region for me.
Later I construct the Alignments track with ylim = c(0,max(x$"22"))). Please take a look at the attached end plot. The ylim is set correctly, but the coverage never seem to get close to 300...
Also, please notice a weird, isolated grey dot in the middle of the plot.
Could you please help me out how to get rid of it and why the max coverage on the plot looks different from the calculated one?
Gviz applies a bit of smoothing in order to make the coverage plot look a bit more appealing:
There's a bit of logic flaw in that it uses the actual coverage range for ylim, and not the smoothed range. Also I can see that having the ability to turn the smoothing off would be beneficial. Not currently do-able, but we can expose that with the next release.
Florian