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statdivlab / corncob

Count Regression for Correlated Observations with the Beta-binomial
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plot options #144

Open jorondo1 opened 1 year ago

jorondo1 commented 1 year ago

Hi! I've been playing around with corncob and I can't figure out how to properly format the plots. The plot() function somehow stitches together all taxonomic levels from the taxonomy. Can we prevent it from doing that? Rplot My ps object is not formatted this way (row.names are species only) so I don't understand that it would stitch all the info from the tax_table columns like that since I already have unique row identifiers.

Also, is there a way to feed the differentialTest output in ggplot to make them more flexible? I'm far from being an R expert so the answer to this might be obvious, but if you have examples to point me to I'd be very thankful.

Cheers !

jorondo1 commented 1 year ago

Hi again. After searching through the source codes I realised there was more than just the plot() function.

I would suggest you specify plot.differentialTest in the vignettes so it's easier to find help, since ?plot doesn't show the help file for these functions.

Cheers,

adw96 commented 2 weeks ago

That’s a good point, @jorondo1 ! We should definitely have an example of this in a vignette.

@gthopkins this should be easy — would you mind updating the vignettes to include an example of how we can do plotting, and how users can get the data that they need out of a summary table to make their own custom plots. This is not urgent, but would be good to have wrapped up within the next 2-3 weeks.

gthopkins commented 2 weeks ago

@adw96 yes, I will update the corncob vignette accordingly. Thank you for describing the timeline on this!