Indicate duplication event on synteny plot?

[erika-r-moore]

Hello!

I am wanting to show a triplication event between different species in a synteny plot, similar to the figure posted in #642. The gene depth ratio between my two species are 1:3, so I believe that means there has been a triplication event. Also, I believe I can see a triplication event within my plot:

Given this, how can I pinpoint which genes are triplicated and highlight only them in my synteny plot?

Some code that may be relevant:

python -m jcvi.compara.catalog ortholog sp1 sp2 --no_strip_names
python -m jcvi.compara.synteny depth --histogram sp1.sp2.lifted.anchors

Also, I tried to do the blocks and microsynteny, but it did not work out:

python -m jcvi.compara.synteny mcscan sp1.bed sp1.sp2.lifted.anchors --iter=3 -o sp1.sp2.i3.blocks
python -m jcvi.formats.bed merge sp1.bed sp2.bed -o sp1.sp2.bed
python -m jcvi.graphics.synteny sp1.sp2.i3.blocks sp1.sp2.bed blocks.layout

blocks.layout:

# x,   y, rotation,   ha,     va,   color, ratio,            label
0.5,	0.6,	0,	center,	top,	m,	1,	sp1
0.1,	0.2,	0,	center,	bottom,	#fc8d62,	.3,	sp2
0.5,	0.2,	0,	center,	bottom,	#fc8d62,	.3,	sp2
0.9,	0.2,	0,	center,	bottom,	#fc8d62,	.3,	Acicarpha
# edges
e,	0,	1
e,	1,	2
e,	2,	3

I am happy to provide more information, I am just unsure what you would need to help with this.

Thanks,
Erika

[tanghaibao]

@erika-r-moore

The highlights in #642 were manual highlights. There is no automated way as far as I know.

My recommended path is to identify (e.g. in EXCEL) a region that visually match 3 regions in sp1.sp2.i3.blocks and then look for the same sp1 region in sp1.sp2.anchors.simple.

You can then add the highlight in front of those blocks, as suggested in the wiki.