Update RDA example using plotLoadings #603
Open
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
antagomir
reviewed
Aug 27, 2024
Comment on lines
+616
to
+617
| #Create a plot | ||
| plotLoadings(coef, ncomponents = 1, n = 20) + labs(x = "", y= "", title = "Top Taxa") + |
There was a problem hiding this comment.
Hmm - why this doesn't use TreeSE directly (but coef)?
There was a problem hiding this comment.
Btw, I think the plotted values are species scores (the coordinate of taxon in ordination space) instead of loadings (how much environmental variable, e.g, diagnosis affects the coordinates). The example has been incorrect
There was a problem hiding this comment.
It's because loadings are not stored in the "rotation" or "loadings" attribute (discussed in #604 )
It requires a wrapper I believe?
There was a problem hiding this comment.
There is a small problem in addRDA as it should store the results to this slot microbiome/mia#634
Let's keep this PR open until the mia is fixed
| ggplot(df, aes(x = x, y = y)) + | ||
| geom_bar(stat = "identity") + | ||
| labs(x = "", y= "", title = "Top Taxa") + | ||
| #Create a plot |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Small update to use new plotLoadings function.
Also shows how to retrieve and plot the loadings for RDA (microbiome/mia#604)
Created same plot as before (can change to plot all components and/or more examples using different parameters/methods)