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I would like to make a convex hull connecting all outermost points for a single `Location` as well as fill by `Location`. Here is what I have so far:
```
# Transform data to proportions for Bray…
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With PCA, it is possible to get the contribution of the genes to the different axes. Is there a way to get this information with the PCoA of CIDR?
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to make it easier to identify samples that are outliers most likely due to high number of missing values.
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Everything was working fine but now the plot.ordination function is showing the following error:
`plot.ordination(ord.res2, method="PCoA", pvalue.cutoff=0.05, show.pvalues=T)`
`Error in ordiellips…
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Often times the colors used for the spheres in the PCoA plot are likely to be the ones that will be used in the animation, if that's the case colors should be matched.
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We can extract feature projection as feature importance in PC1 axis, such as the "components_" attribute in https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.PCA.html
How can …
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Noting that the more data we add some of these plots will be changing (PCoA) and that once the data is re-picked with more recent versions of the GreenGenes database some of the taxonomic assignments …
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A group of samples should be capable of creating an ellipsoid centered at the centroid of all the points and with a volume given either by the standard deviation or the standard error. Some related co…
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Feature request please - It would be great if jackknifed_beta_diversity.py could output tab-separated files summarizing the data that are plotted in the PCoA plots. E.g., one text file of tab-separate…
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Hi, I am trying to run plot_ordination but I keep getting a warning and then the object is just NULL. I have ran this code hundreds of times before and it worked perfectly, so I really don't understan…