-
We should enhance the `PCADecomposition` visualizer to provide many of the features the `Manifold` visualizer provides, including things like:
- [ ] Color points by class with a legend (See #458)
…
-
should we flag new users about problems with possible colinearity issues if their metadata categories are too similar (e.g. including a continuous value of BMI and a quartile category of BMI)?
-
Used to have these in the package and at some point removed them but now think they should be back
-
Currently the plots as created by plot_ordination are incorrect from a biplot perspective.
If you compare what comes out of dudi.coa, a standard correspondence analysis biplot
with the example data ma…
-
## background
[Gower &al (2011)](https://www.wiley.com/en-us/Understanding+Biplots-p-9780470012550) detail several measures of fit for biplots, most prominently
* the _quality_ of the $r$-dimens…
-
Dear @jfukuyama,
I would like to use `adaptiveGPCA` to analyze a marine microbiome data set and explore the environmental drivers of community composition. A similar example but using PCoA can be f…
-
Would be great to have the loadings associated with each OTU from a PCoA to better explore the taxonomic differences between samples/treatments. This can also be done by comparing OTU abundances with…
-
## Summary
Thanks for the great package!
Currently, the repel works to repel text away from single points. However, it would be great if it could repel text away from segments as well. This wou…
-
Hello,
I've read
https://github.com/sib-swiss/dsSwissKnife-example/blob/main/dsSwissKnife_example.R
And I successfully performed PCA and KNN.
Now I want to plot the first two PCA components us…
-
A geom layer `geom_u_projection(from = i, to = j)` should render a (by default dashed) line from the ordinates of the `i`th row of $U$ to the linear subspace containing those of the `j`th row of $V$, …