Expand scale_fill_brew palette in pafr

[aaronphillips7493]

Hey,

I have 13 query sequences that I am trying to visualise aligned to 12 reference chromosomes.

I am trying to use:
plot_coverage(prim_alignment, fill='qname') + scale_fill_brewer(palette="Set3")
but, as I have 13 qnames and Set3 only contains 12 colours, one of my sequences is not coloured.

Is there a way to fix this? I have tried looking at this:
https://www.r-bloggers.com/2013/09/how-to-expand-color-palette-with-ggplot-and-rcolorbrewer/

but to no avail.

Any advice?

Thanks,
Aaron :)

[SamCT]

Also curious about this. I have an alignment file with several hundred contigs, would like to introduce some sort of color palette that can account for that but I am limited to an arbitrary 12. Is there a way to create my own color palette? I can widdle down the contig list to those of a certain length, and I've seen a pallette with 256 colorways. In general color pallets seem to be limited ~20. When I run the plot coverage on hundreds of contigs vs ~16 large (chromosome) contigs, I just get a image that looks like spiral-notebook paper. Maybe the devs have a suggestion for this?

Thank you