PCoA - can you mark samples from the plot?

[Sam Noel]

Hello,

I have generated PCoA plots from my data and I can see separation into groups that isn't explained by any of my metadata. I was wondering if there is a way to mark the samples and export a list from the PCoA plots so I can go back and see if I can find an explanation for the grouping? I realize I can show the sample names on the plot but there are far to many for me to read.

Thanks you

Sam

[Colin Brislawn]

Hello Sam,

I don't think there is a super elegant way to do this, like the list export you mentioned. I think turning on labels, like you mentioned, if your best bet. You could also try using the Visibility tab to 'turn off' some of the points so you can the ones you want. 

Let me know what you find Sam,

Colin

[Jamie Morton]

Colin is right.  There is not convenient with the current Emperor interface.

However --- we are getting close to pushing out a new version of Emperor.  So if you have improvements you'd like to see, or even better, push in some code directly into Emperor, feel free to open up an issue, or push a pull request on Emperor's github page.  We'll warmly welcome any contributions.

Cheers,

Jamie

[Sam Noel]

Thanks Colin,

Turning on the labels won't work for me, I have 800 samples and they are too close to read the labels. Is there another way to do this, perhaps directly from the distance matrix file?

Sam

[Sam Noel]

Thanks for the advise I found how to do what I want using the unifrac_pc file. In excel sorting on the columns will provide a list of samples separated along PC2 and PC3.

Sam

[Colin Brislawn]

Glad you figured it out, Sam. And thank you for posting the solution so that other folks can find it.

Colin