Scale on ribbon about gggenomes HOT 4 OPEN

Fancy! Good question. What kind of scale do you mean? A complete axis, or a small scale bar with fixed size for comparison. Maybe akin to #85 geom_scale_bar but on the y-axis matching the ribbon scale?

On a side note, check out gggenomes::geom_wiggle() which I've added a while back. It wraps geom_ribbon(), so that you don't need to add all the y,ymax,x,xend, ....

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Thanks a lot for the geom_wiggle() tip! Indeed makes it much easier to plot the ribbons. I tried the "line" and "linerange" option which gives you a legend for the plotted data. This is already pretty nice!
Below is the "line" version as I think the "linerange" is a bit confusing in a whole genome context. To elaborate the graph a bit: The upper ribbon is actual annotated genes of a gene family and the lower part is expressed genes of the same gene family from IsoSeq data.

However, the problem I encounter is that each ribbon gets its own legend scale. It should be a shared one among all the ribbons.

I guess an added dedicated axis for each ribbon would be the easiest for people to understand what they are looking at there.

Thank you for your help!

Cheers,
Daniel

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A little update to this. I had some time to play around with this and I got a bit further with the gggenomes builtin aesthetics:

• First I draw the bare genome
• Then I add the feature track plus a bar plot
• To this I add the axis information plus a continuous scale that takes the max from the added feature track.

p_chr <- gggenomes(seqs = genome)+
  geom_seq()

p_chr %>% add_feats(cluster)+
  geom_bar(aes(x=(x+xend)/2,
               y = score), 
              feats(cluster),
              fill="orange",
              linetype=1,
              size=0.1,
              alpha=1, 
              stat = "identity")+
  theme(axis.line.y.left = element_line(),
        axis.ticks.y = element_line(),
        axis.text.y = element_text(),
        axis.line.x = element_blank(),
        axis.ticks.x = element_blank(),
        axis.text.x = element_blank())+
  scale_y_continuous(limits = c(0, max(cluster$score)),breaks = seq(0,max(cluster$score), 2))

My question would be if there is a way to move the bare genome to 0. It seems to sit always at 1 at the Y-axis.
I haven't tried to add this to a bigger gggenomes plot.

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Here's a solution, although granted, not the prettiest ...

p1 <- gggenomes(emale_genes, emale_seqs) |> add_clusters(emale_cogs) +
  geom_seq() + geom_gene()

# default plot with first genome at y==1
p1 + theme_bw()

p2 <- p1
# change y-coords of seqs by hand
p2 <- set_seqs(p2, get_seqs(p2) |> mutate(y=y-1)) 
# relayout other features (genes, etc)
# BUG: this should work but ignore_seqs not propaged
# p2 <- layout(p2, ignore_seqs=TRUE) 
# this works
p2$data <- layout(p2$data, ignore_seqs=TRUE)

# plot with genomes shifted on y axis, i.e. first genomes at y==0
p2 + theme_bw()

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