Question regarding geom_link

[hkaspersen]

Hello, and thanks for an awesome tool!

I have a question regarding geom_link. I tried to figure out what it's actually plotting. Is the links' fillcolour based on a variable in the paf file? Trying to figure out which values are used here. I couldn't see it in the .R file for geom_link. I am assuming it is some sort of sequence similarity?

Thanks in advance!

[thackl]

If you don't set a fill aesthetic, the default fill/color is just a fixed grayish value with some transparency so it is easier to spot overlaps: aes(colour = "honeydew3", fill = "honeydew3", size = 0.5, linetype = 1, alpha = 0.7).

gggenomes(seqs=emale_seqs, links=emale_ava) + geom_link()

But you can set fill, alpha, etc. to a variable, based on the data in your link table. For example:

# color links by match identity
gggenomes(seqs=emale_seqs, links=emale_ava) +
  geom_link(aes(fill=map_match/map_length))

[hkaspersen]

Thank you for a quick reply! This works for me. However when I combine it with geom_gene I get the follwing error:

gggenomes(seqs=emale_seqs, links=emale_ava, genes = emale_genes) +
  geom_link(aes(fill=map_match/map_length)) +
  geom_gene(aes(fill = name))

Error: Discrete value supplied to continuous scale

Any thoughts on this?

Edit: I did manage to get it to work with ggnewscale, as it seems to be an issue with a discrete and continuous fill variable:

library(ggnewscale)

gggenomes(seqs=emale_seqs, links=emale_ava, genes = emale_genes) +
  geom_link(aes(fill=map_match/map_length)) +
  new_scale("fill") +
  geom_gene(aes(fill = name))

[thackl]

Ah, yes. Using fill with multiple variables in the same plot is something that by design does not really work with ggplot. But there are workarounds, such as ggnewscale. The general ggplot idea is that two many different color scales make the plot too hard to understand. I usually try to follow that notion, and try to use color for the feature I want to primarily highlight. I use, for example, color for genes and than grey scales using alpha for link identity...

[erosminer]

Hi!

I have a question regarding the border in geom_link. It seems that it can't change the color of the border when changing the fill color of link. I wonder if it can set the size, color and presence of the border.

Thank you very much!