How do I export a KaryoploteR plot or insert it into a grid/lattice? Can I assign a KaryoploteR plot to a variable?
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6 weeks ago
Andrew • 0

I've generated some KaryoploteR plots I want to use, but I have a lot of them to handle. I'd like to be able to organize them in a grid or at least export them in code. But if I assign the output to a variable, it seems like it just assigns parameter data and doesn't assign a graphical object to the parameter.

I looked through the code, and it appears to call graphics::plot() to generate the graphics. I'm not super familiar with the underlying graphics handling in R. Is there a way to assign KaryoploteR plots to figures so I can plot them within a grid or export them using the png or tiff saving functions?

karyoploteR grid ideograms • 349 views
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Thank you for explaining the issue in detail. It would help if you could post some example code where help is needed.

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6 weeks ago
Lisa Ha ▴ 120

I had the same question recently and just found this blog post which looks very promising: Save base graphics as pseudo objects in R. It describes two approaches for base graphics, although one is based on a now obsolete package (pryr). The current implementation seems to be tidyeval. I haven't tried it yet, but it looks like what you need.

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I just found this on the karyoplotr github page: ggplotify or grid to use karyoplotr images in multipanel layouts

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6 weeks ago
Andrew • 0

Code:

kp <- plotKaryotype(plot.type = 1, chromosomes = c("chr1", "chr2", "chr3", "chr4"))

That outputs a graphics object directly. It doesn't save it to any variable. However, I've made some progress:

x <- recordPlot(load=NULL, attach=NULL)``

recordPlot() will take whatever has been output to the graphics viewport and save it. Then I can capture that using as_grob:

aGrob <- as_grob(x)

That gets me pretty far. I can now save karyoplots to a list, and I can call them and save them as pngs. What I'd like to do is rotate them and arrange them in a grid, though.

I can rotate them with:

aGrob <- editGrob(aGrob, vp=viewport(angle=-90))    

However, I still can't plot them in a grid. Currently, when I try, I get a lot of errors and plots are missing. It might not be obvious, but in the image below, there is a big empty space where Chr1 should be.

grid.arrange(plotList[[1]], nrow = 1)

will produce the following: enter image description here

but

grid.arrange(plotList[[1]], plotList[[2]], nrow = 1)

produces: enter image description here

It reports the following errors:

Warning messages: 1: In grid.Call.graphics(C_setviewport, vp, TRUE) : cannot clip to rotated viewport

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