kpPlotDensity log scaling?

[aboyd003]

Hi all,

Is there any method to log scale the values for the density plot? Ie I want the entire track output by kpPlotDensity to be on log scale. I read through the documentation and did not find anything referencing log scaling with respect to kpPlotDensity.

[bernatgel]

Hi @aboyd003

It is indeed not possible to set up a log scale for kpPlotDensity. To do it right, we should probably use the log capabilities of base R and implement it through the whole lot of plotting functions, and adapt also kpAxis to reflect that. It's doable, but not in a short time frame.

If you really need it now, your best option would be to create your own version of kpPlotDensity function (its only 16 lines of code) and make compute the log of the density before plotting. This should work (untested!)

"""
myLogKpPlotDensity <- function (karyoplot, data = NULL, window.size = 1e+06, ymin = NULL,
ymax = NULL, data.panel = 1, r0 = NULL, r1 = NULL, clipping = TRUE,
...)
{
if (!methods::is(karyoplot, "KaryoPlot"))
stop(paste0("In kpPlotDensity: 'karyoplot' must be a valid 'KaryoPlot' object"))
if (!methods::is(data, "GRanges"))
stop(paste0("In kpPlotDensity: 'data' must be a valid 'GRanges' object"))
windows <- tileGenome(karyoplot$chromosome.length, tilewidth = window.size,
cut.last.tile.in.chrom = TRUE)
dens <- GenomicRanges::countOverlaps(windows, data)

#MODIFIED CODE
dens <- log(x=dens, base=10)
#END MODIFIED CODE

if (is.null(ymax)) {
    ymax <- max(dens)
}
karyoplot <- kpPlotRibbon(karyoplot, data = windows, y0 = 0, 
    y1 = dens, ymin = ymin, ymax = ymax, data.panel = data.panel, 
    r0 = r0, r1 = r1, clipping = clipping, ...)
karyoplot$latest.plot <- list(funct = "kpPlotDensity", computed.values = list(density = dens, 
    windows = windows, max.density = max(dens)))
invisible(karyoplot)

}

"""

and then adjust the axis. If for the axis you get the maximum value from kp$latestplot... it will be already in log scale. If you compute it before plotting, then remember to take the log too.

Hope this helps

Bernat

[aboyd003]

Thank you.
I used your modified function :) and used it to modify the kpPlotBAMDensity function as well :)

[bernatgel]

Great! glad that helped! I've added the log scale to the list of future enhancements, but much better if you do not need to wait for me! Bernat El jue, 17 oct 2024 a las 14:51, AMBoyd ***@***.***>) escribió:

…

Thank you. I used your modified function :) and used it to modify the kpPlotBAMDensity function as well :) — Reply to this email directly, view it on GitHub <#156 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAHAPQOX2SD3AVAFQEPDMATZ36XGNAVCNFSM6AAAAABQCTEH7OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMJZGQ3DENJXGU> . You are receiving this because you were assigned.Message ID: ***@***.***>