2
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I am curious how people make genome track plots such as what can be done with the Bioconductor package ggbio.

For example this plot was made w/ ggbio: enter image description here

I think ggbio is great for making fast plots, but it is kind of a pain to make publication quality figures because it is hard to manipulate the plots after they are constructed. Normally I would use ggplot2 to customize the plot extensively, but it doesn't work very well after plotting with ggbio.

How can I use ggbio for these types of plots? Is there a better tool instead?

EDIT: I would get the legends for each individual plot and combine them before adding back to the main plot using something like this:

leg1.grob = cowplot::get_legend(plot1)
leg2.grob = cowplot::get_legend(plot2)
sharedleg.grob = gridExtra::gtable_rbind(leg1,leg2)

mainplot.grob = ggplotGrob(main_plot)
mainplot.grob = gtable_add_cols(mainplot.grob, 
                                widths = sum(sharedleg.grob$widths))
mainplot.grob = gtable_add_grobs(mainplot.grob, 
                                 grobs = sharedleg.grob, 
                                 t=t,b=b,l=l,r=r)
cowplot::ggdraw(mainplot.grob)
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  • 1
    $\begingroup$ Could you expand on "hard to manipulate the plots". What is the expected output? I mainly use ggbio for gene track and to merge multiple plots vertically, x-axis aligned. $\endgroup$ – zx8754 May 21 '18 at 9:35
  • $\begingroup$ The "hard to manipulate" part is that ggbio constructed plots do not return a ggplot or gtable object. I can access the grobs from a ggbio tracks object, but they won't be aligned as they would be in the final plot. I like to make shared legends and include them in the plot, and without having a gtable or ggplot object it is hard to add the shared legends in, and I end up having to save them as a separate file which is tedious. EDIT: FYI I mainly use ggbio for the same purposes as you - gene tracks + x-axis alignment $\endgroup$ – Reilstein May 21 '18 at 18:25
  • $\begingroup$ So the question is: how do we make ggbio shared legend? At the moment I use custom/manual legends like you are doing. $\endgroup$ – zx8754 May 21 '18 at 18:54
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    $\begingroup$ I added the process I would use to create the shared legend, is that what you mean? $\endgroup$ – Reilstein May 21 '18 at 19:15
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    $\begingroup$ I like gviz bioconductor.org/packages/release/bioc/html/Gviz.html $\endgroup$ – Chris_Rands May 23 '18 at 8:40
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It seems like the ggbio object already contains the corresponding ggplot object. You should be able to extract the ggplot from the ggbio_obj@ggplot slot and extract your gtables.

Small example:

library(ggbio)
library(ggplot2)
library(patchwork)

fl.bam <- system.file("extdata", "wg-brca1.sorted.bam", package = "biovizBase")
wh <- as(c("chr17:41239394-41319151:+"), "GRanges")
p_cov <- autoplot(fl.bam, which = wh)
#> reading in as Bamfile
#> Parsing raw coverage...
#> Read GAlignments from BamFile...
#> extracting information...


df <-  data.frame(x= sample(1:100,size = 100,replace = TRUE))
p_hist <- ggplot(df) + 
    geom_histogram(aes(x))


p_hist / p_cov
#> Error: Can't add `e2` to a ggplot object.
#> Backtrace:
#>     █
#>  1. └─patchwork:::`/.ggplot`(p_hist, p_cov)
#>  2.   └─GGally:::`+.gg`(e1, e2)
#>  3.     └─e1 %+% e2
#>  4.       └─ggplot2:::add_ggplot(e1, e2, e2name)
#>  5.         ├─ggplot2::ggplot_add(object, p, objectname)
#>  6.         └─ggplot2:::ggplot_add.default(object, p, objectname)

p_hist / p_cov@ggplot
#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

Created on 2021-02-05 by the reprex package (v1.0.0)

Session info

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5
  • $\begingroup$ Does this answer the question? I think OP asked about plotting gene models with ggbio or an alternative tool. $\endgroup$ – Kamil S Jaron Feb 5 at 14:10
  • $\begingroup$ Based on the OP's comment below his question I assumed he wanted to know how to extract a the ggplot2 part out of a ggbio object. With this he should be able to make further adjustments to the figure. $\endgroup$ – Alex Feb 6 at 17:25
  • $\begingroup$ Ah, I did not go through the stack of the comments. The answer makes much more sense now. $\endgroup$ – Kamil S Jaron Feb 7 at 13:43
  • 1
    $\begingroup$ @Alex Does this solution work when aligning multiple genome tracks using ggbio as in my original example? Either way, useful info for others. My original question was actually aiming to get feedback on how others make these types of plots rather than seeking a solution to a specific problem in my workflow, so if you have any thoughts on that I'd be interested $\endgroup$ – Reilstein Feb 7 at 23:22
  • $\begingroup$ @Reilstein this solution requires more work to align multiple genome tracks based on coordinates, so actually does not really answer your initial question. I was using Gviz before, but I like ggbio more due to the ease of use and how it integrates with ggplot2. $\endgroup$ – Alex Feb 8 at 8:37

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