I need to render 2D PCoA plots with confidence ellipsoids. After going through help forum posts here I found others looking to do the same and roadmap plans from 2017 to add this functionality--it seemed that this had been added. I generated a jackknifed Emperor plot using "qiime diversity beta-rare…

@John_Blazier , Good question — skip to the bottom of my post to see the answer! QIIME 2 does not really have a way to make 2D plots with ellipsoids (yet). [image] John_Blazier: I exported the data from this visualization.qzv file using “qiime tools export” and then tried to render the 2D plot …

Thank you, this looks very helpful! The code in the tutorial you linked runs fine--all the data imports and looks right. When I try to draw the plot with the code you posted here I get this error: Joining, by = "#SampleID" Joining, by = "#SampleID" Error: Can't join on '#SampleID' x '#SampleID' …

[image] John_Blazier: The code in the tutorial you linked runs fine–all the data imports and looks right. When I try to draw the plot with the code you posted here I get this error: The code I posted was just copied from the tutorial, with the stat_ellipse() line added to the end, so I am not…

Hi Nicholas, That R code worked great as soon as I replaced the numeric sample IDs with alphanumeric ones. Thank you so much. [D_MvF_weighted_shannon_image]

Nicholas, have you ever tried to calculate a p-value for the separate clustering of groups in one of these 2D PCoA scatter plots? I have several of these scatterplots with 2-4 groups, now with nice confidence ellipsoids. Some of the groups have almost/barely overlapping confidence ellipsoids, and my…

@John_Blazier , The proper way to do this would be with a PERMANOVA test. See: qiime diversity beta-group-significance qiime diversity adonis

Thanks, Nicholas. That's kind of what I thought. It seemed like they were probably conflating two different analyses.

Hello John, Do you mind sharing how you put the % for each axis? I finished my plot but need to put on the percentage for each axis. Thanks

Hi @Bing , [image] Bing: Do you mind sharing how you put the % for each axis? That's all in the code I posted above: [image] PCoA plots with confidence ellipsoids Technical Support @John_Blazier , Good question — skip to the bottom of my post to see the answer! QIIM…

Thanks. This really helps a lot.

QIIME 2 Forum

PCoA plots with confidence ellipsoids

Technical Support

show post in topic

Home
Categories
Guidelines
Terms of Service
Privacy Policy

Powered by Discourse, best viewed with JavaScript enabled