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How to plot region as in Fig 3E in Lovell et al eLife 11:e78526 #99

Closed matt-shenton closed 1 year ago

matt-shenton commented 1 year ago

HI there,

Thanks for the great tool.

I may be being foolish, but I'm struggling to find how to make a sub-chromosomal region riparian plot like Fig3E in the paper. Or was that done outside the package?

Many thanks for your help

Matt Shenton

jtlovell commented 1 year ago

That is done with the riparian plotting function ... see section 5.2 of the tutorial here

matt-shenton commented 1 year ago

Thanks for your response. My problem was that I didn't realise I need to specify all the genomes in the roi. I only specified the position in the reference genome, then the whole chromosome was displayed for all the genomes. Now I realized that if I specify all genomes with their appropriate syntenic regions, then I can get the plot I wanted. Thanks for your help, and sorry for bothering you. Best wishes Matt Shenton

matt-shenton commented 1 year ago

Further to the last comment - if I use " useOrder = FALSE" in the plot_riparian function, the whole chromosome is displayed again. Anyway, thanks again, Matt