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jtlovell / GENESPACE

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riparian plots are inconsistent #149

Closed gorliver closed 2 months ago

gorliver commented 4 months ago

Thank you for the tool! I have successfully run GENESPACE using ten genomes, and the riparian plot looks nice. Here's a screenshot with two genomes. image

However, if I plot a new riparian plot of just the two genomes, use the following command:

ripd <- plot_riparian(gsParam = out,genomeIDs=new2run[c(13,14)],refGenome = "tomato", useRegions = FALSE,useOrder=FALSE)

The riparian plot looks very different: image

Several blocks were missed in the new riparian plot. Did I need to include anything in the parameters?

jtlovell commented 2 months ago

I think you are using regions on the top and blocks on the bottom. regions average across positions that may lack alignments (e.g. pericentromers on chr01)

gorliver commented 2 months ago

I see. Many thanks!