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jtlovell / GENESPACE

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Missing one chromosome on the riparian plot #123

Closed jacquelinemattos closed 9 months ago

jacquelinemattos commented 1 year ago

Hi, First of all, thanks for such an amazing program!

I am having a little trouble understanding what's happenning with my plots. My species has 12 chromosomes, and I want to plot them all (comparing with two other species with different chromosome numbers). I used the parameter: "minChrLen2plot = 0" that is said to include all (even tiny) chromosomes/scaffolds. Still, chromosome 9 in my species doesn't appear in my plot. Is there something to correct? I'm pasting my code for the riparian plot here. Thank you very much!!

ripDat <- plot_riparian( gsParam = out, refGenome = "Epidendrum", genomeIDs = c("Dendrobium", "Epidendrum", "Vanilla"), forceRecalcBlocks = FALSE, useOrder = FALSE, useRegions = FALSE, minChrLen2plot = 0, palette = customPal, braidAlpha = .75, chrFill = "lightgrey", addThemes = ggthemes)

jtlovell commented 11 months ago

Sorry about the delayed response - so ... my guess is one of your chromosomes doesn't have any synteny (for example, the Y chromosome doesn't show up in mammalian synteny maps).