Rotated or staggered chromosome label, las argument?

[zx8754]

I looked through the karyoploteR tutorials couldn't find solution, apologies if this was already implemented.

When we plot as below, the chromosome labels overlap for chr17 to chr22

kp <- plotKaryotype(genome = "hg19", plot.type = 4,)
kpDataBackground(kp)

Any chance we could have labels vertical, as in las = 3 in base R:

las numeric in {0,1,2,3}; the style of axis labels. 0: always parallel to the axis [default], 1: always horizontal, 2: always perpendicular to the axis, 3: always vertical.

Alternatively, have it staggered?

[zx8754]

OK, found it, of course it is implemented, srt = 90 would rotate it:

kp <- plotKaryotype(genome = "hg19", plot.type = 4, srt = 90)
kpDataBackground(kp)

Any chance we can have staggered option?

[bernatgel]

Hi @zx8754

Glad you found a solution. I usually use 45 degrees instead of 90, but it's a question of preferences. Also, take into account that that srt will also rotate the main title if there is one!

I had not thought about the staggered option, which makes a lot of sense. I'm pretty sure you can achieve this with a bit of hacking right now:

You should:

• call plotKaryotype with "labels.plotter=NULL", so we plot the chromosome names independently with more control
• Then call kpAddChromsomeNames twice, one with the odd names and one with the even ones, adjusting the y position as needed

Something along the lines of

library(karyoploteR)

kp <- plotKaryotype(genome = "hg19", plot.type=4, labels.plotter=NULL)

evens <- ((1:length(chr.names))%%2)==0

chr.names <- kp$chromosomes
even.names <- chr.names
even.names[!evens] <- ""

odd.names <- chr.names
odd.names[evens] <- ""

kpAddChromosomeNames(kp, chr.names = odd.names)
kpAddChromosomeNames(kp, chr.names = even.names, yoffset = -10)

You can also modify the names vector to remove "chr", etc... If you have any problem with this, please ask

In any case, I'll log the request for the staggered option for future developments :)

Thanks!