Feature request: automatically minimize number of inversions plotted?

[taprs]

Hi John,

Thanks for the wonderful tool! It is a true pleasure to use it.

I plot synteny between a few de novo assemblies which have random orientation of contigs. I would be happy to have an option to plot_riparian() that would invert the contigs in the non-reference assemblies to minimize the number of "inversions" in the plot. I guess all the required information is already being produced by the package; would it be possible to implement that?

Regardless of the answer, thank you! You have already done an amazing job. Best, Nikita

[sashulkaSh]

invertTheseChrs: data.table with two columns, genome and chr containing the lists of genomes and chromosomes that should be inverted in the plot. Not currently implemented.

[taprs]

Thanks for your input @sashulkaSh!

I think the new part in my request has to do with the word 'automatic'. Imagine aligning ten draft assemblies with 20 randomly directed chromosomes in each... I would be happy with an implementation through invertTheseChrs too if I was given a way to generate this data.table automatically.

So far I ended up inverting the chromosomes according to reference in each assembly before running GENESPACE. Also doable but less convenient.

[sashulkaSh]

@taprs I agree, it would be convenient

[jtlovell]

Sorry about the delayed response - so, an option to automatically use invertTheseChrs when >50% of the chromosome is inverted relative to the reference? not a bad idea.