Geom_ribbon simple example

[olekto]

Hi, I feel a stupid asking this, because this is likely an R issue, and not necessary gggenomes. What I want to do is to plot something similar to the GC plot from the example, the geom_ribbon. I've tried trimming down the example to just the seqences, links and the GC ribbon, but I get an error.

I basically want this, and then add ribbon:

gggenomes(seq=emale_seqs, links=emale_ava, feats=emale_gc) +
  geom_seq() +
  geom_bin_label() +
  geom_link() 

Adding

 + geom_ribbon(aes(x=(x+xend)/2, ymax=y+.24, ymin=y+.38-(.4*score), group=seq_id),
            feats(emale_gc))

to that example doesn't work (Error: Can't convert a spec_tbl_df/tbl_df/tbl/data.frame object to a string). I'm not fluent in R, and have to wrangle with it every time I need to do something a bit more complicated. I might be getting old, but it is not straight forward to understand the error messages and the language itself.

Any help would be highly appreciated.

Thank you.

Ole

[thackl]

Try geom_wiggle(). It's a wrapper around ribbon that is much easier to use with gggenomes data.

[thackl]

The issue with your ribbon example is how you refer to the GC data. When adding to the gggenomes object, you are labeling the track with a track_id. In your case the track_id is "feats" because you wrote `"feats"=emale_gc. You need to use this track_id when referring to the data

p <- gggenomes(seq=emale_seqs, links=emale_ava, feats=emale_gc) +
  geom_seq() +
  geom_bin_label() +
  geom_link()

p %>% track_info() # show tracks with track_ids

p + geom_ribbon(aes(x=(x+xend)/2, ymax=y+.24, ymin=y+.38-(.4*score), group=seq_id),
            feats()) ## default feat track name for feats is "feats"

# Alternatively feats with custom different track_id 
gggenomes(seq=emale_seqs, links=emale_ava, feats=list(emale_gc)) + 
  geom_ribbon(aes(x=(x+xend)/2, ymax=y+.24, ymin=y+.38-(.4*score), group=seq_id),
            feats(emale_gc) ## emale_gc added with track name "emale_gc"

[olekto]

Thank you!

And thank you for the prompt answer.

Ole