Adjust gene position in plot according to orf

[SergejRuff]

ggggenomes allows to change position of orfs via

geom_feat(size = 3,position = "pile")

But how do I change the position of the genes in geom_gene() to make sure the ORF and genes allign?
position="pile" doesnt do the same thing.

[SergejRuff]

Here is what I mean: The genes in the first contig with the longet length do not match the orf position as some are elevated.

The code i use:

gggenomes(seqs = s0, genes = g0, feats = orf0) +
  geom_feat(size = 3,position = "pile") +
  geom_seq() +
  geom_gene(aes(fill = interpro_description))  +
  # geom_gene(data = genes(g0_filtered),aes(fill = interpro_description))  +
  # geom_gene(aes(fill = interpro_description),position = position_strand(flip = FALSE, base = 0.1))  +
  theme(plot.margin = margin(1, 1, 1, 1, "cm")) +
  theme(legend.position = "bottom", axis.text.x = element_text(size = 10)) +
  scale_x_continuous(labels = function(x) format(x, big.mark = ",", scientific = FALSE),
                     breaks = c(0, 5000, 10000, 15000, 20000, 25000,30000) )

[thackl]

Unfortunately, it is not possible to automatically have the genes match the position of the ORF when using "pile". Piling is run on each geom layer independently, so geom_gene does not know where ORFs placed by geom_feat end up.

If you want all ORFs on the same line (as the genes), you can set position="identity", and for example, change the coloring of the ORFs

#| fig-height: 1
#| fig-width: 8
library(tidyverse)
library(gggenomes)

g0 <- tibble(seq_id = "foo", start=c(10,100,200,400,500), end=start +60)
orfs <- tibble(seq_id="foo", start=c(10, 200, 400), end=c(200, 400, 560)) |> 
  mutate(orf_id=paste0("orf", row_number()), alternate=row_number() %%2)

gggenomes(g0, feats=orfs) +
  geom_feat(aes(color=alternate), position="identity", size=5, alpha=.3) +
  geom_gene()

And if you know the orf_id for each gene, you can manually set alternating positions for ORFs and genes consistently.

#| fig-height: 1
#| fig-width: 8
g1_with_orf_id <- g0 |> mutate(
  orf_id = paste0("orf", c(1,1,2,3,3))) |> 
  left_join(select(orfs, orf_id, alternate))

gggenomes(g1_with_orf_id, feats=orfs) +
  geom_feat(aes(y=y+0.4*alternate, yend=y+0.4*alternate), position="identity", size=5) +
  geom_gene(aes(y=y+0.4*alternate, yend=y+0.4*alternate))

[SergejRuff]

Thanks. What is "alternate" in the second example?

[thackl]

It's that alternating counter that I added to orfs with alternate= row_number %% 2. It's value will alternating between 1 and 0.