Add Chromosome Breaks and Labels to Continuous x-axis in R

Question

[selplat21]

I have a paf file that have imported that has the following structure:

Classes ‘pafr’ and 'data.frame':    44304 obs. of  18 variables:
 $ qname : chr  "Chr1" "Chr1" "Chr1" "Chr1" ...
 $ qlen  : num  196345723 196345723 196345723 196345723 196345723 ...
 $ qstart: num  136822117 180636036 161249961 149012134 155428335 ...
 $ qend  : num  148529244 193071845 177994375 155397308 161194689 ...
 $ strand: chr  "-" "+" "-" "+" ...
 $ tname : chr  "OU015528.1" "OU015528.1" "OU015528.1" "OU015528.1" ...
 $ tlen  : num  82614289 82614289 82614289 82614289 82614289 ...
 $ tstart: num  45642910 65383687 14852200 5070550 59356880 ...
 $ tend  : num  57423515 78622207 32888725 11853840 65371656 ...
 $ nmatch: num  990974 973135 1187463 552523 440276 ...
 $ alen  : num  12799627 14232743 19469502 7228820 6536219 ...
 $ mapq  : num  60 60 60 60 60 60 60 60 60 60 ...
 $ tp    : chr  "P" "P" "P" "P" ...
 $ cm    : num  92453 90044 110220 53963 40657 ...
 $ s1    : num  636113 512050 508620 338152 227618 ...
 $ s2    : num  1135 369 441 147 370 ...
 $ dv    : num  0.0156 0.0169 0.0176 0.0144 0.018 0.0205 0.015 0.0271 0.023 0.0198 ...
 $ rl    : num  1192370 1192370 1192370 1192370 1192370 ...

I've plotted using the following command, but I would like to add another label on the x-axis that would label/delimit chromosomes in addition to the current bp position.:

ggplot(data=bth.paf, aes(x=qstart, xend=qend, y=tstart, yend=tend)) + 
  geom_segment(color="blue") + 
  labs(x="Reference coordinate", y="Query coordinate") + 
  ylim(100000,1000000) +
  geom_rect(aes(xmin=0, xmax=200000000, ymin=782541, ymax=782654), colour=alpha("orange", 0.5), fill.alpha=0.5) + theme_bw()

[zx8754]

Use facet_grid on chromosome column - qname.

[selplat21]

This is definitely what I want, but I have about a hundred scaffolds. So I am trying to have it all in one row such that the visible sections are the larger chromosomes.

[zx8754]

Please read the manuals: https://ggplot2.tidyverse.org/reference/facet_grid.html

We will need something like:

... + facet_grid(qname ~ ., scales = "free_x")