Plotting gene models - alternatives to ggbio

Question

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:

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. I have noticed 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. FYI I mainly use ggbio for gene tracks + x-axis alignment.

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)

I've used gviz before, but long ago. Do you know if you can extract the grid plot grobs of the gene track plots with Gviz?

Answer 1

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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