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Select samples for PCoA #49
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Thank you for the feature request! The reason I didn't include options like Therefore, if the goal is to see how PCoA looks in the absence of certain samples, then you should calculate a new distance matrix and plot it again. This can be easily done within Dokdo and an example of this is illustrated in the
I think there could still be an argument to be made in the favor of adding options like Hope this helps! |
Thanks @sbslee This works perfectly. When I recompute using the function you suggested in the second part of the script I get a plot with warning message like this: What does this actually mean? |
Glad to know that Dokdo is helpful to you! As for the warning, you don't have to worry about it. It simply means that numeric data was converted to boolean (e.g. 442 --> True, and 0 --> False). This conversion was needed because you are using the Jaccard distance as distance metrics, which computes distance between samples based on the presence/absence of microbiome instead of using their abundance. Hope this helps. |
Hi sbslee,
I was using dokdo for plotting PCoA as below:
which is working fine.
But,
I was wondering if we can have function like 'where' or 'include_samples' or 'exclude_samples' or something like that to control the samples to be presented on the plot.
Thanks
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