To Reproduce
uwotplot <- umap_pq(ps, pkg = "uwot",
n_neighbors = 5,
verbose = TRUE)
Console output
Taxa are now in rows.
Joining with `by = join_by(Sample)`
23:12:06 UMAP embedding parameters a = 1.577 b = 0.8951
23:12:06 Read 23 rows and found 9714 numeric columns
23:12:06 Using FNN for neighbor search, n_neighbors = 5
23:12:07 Commencing smooth kNN distance calibration using 6 threads with target n_neighbors = 5
23:12:08 Initializing from normalized Laplacian + noise (using RSpectra)
23:12:08 Range-scaling initial input columns to 0-10
23:12:08 Commencing optimization for 500 epochs, with 150 positive edges using 6 threads
23:12:08 Using rng type: pcg
Using method 'umap'
Optimizing with Adam alpha = 1 beta1 = 0.5 beta2 = 0.9 eps = 1e-07
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
23:12:09 Optimization finished
Joining with `by = join_by(Sample)`
Warning message:
The `x` argument of `as_tibble.matrix()` must have unique column names if `.name_repair` is
omitted as of tibble 2.0.0.
ℹ Using compatibility `.name_repair`.
ℹ The deprecated feature was likely used in the MiscMetabar package.
Please report the issue at <[https://github.com/adrientaudiere/MiscMetabar/issues](vscode-file://vscode-app/Applications/Positron.app/Contents/Resources/app/out/vs/code/electron-browser/workbench/workbench.html#)>.
It appears tibble since 2.0.0 wants users to explicitly use the .name_repair argument to handle non-unique or missing column names. It's probably fine unless they fully defunct this function.
Expected behavior
Complete the process without warning.
To Reproduce
Console output
It appears tibble since 2.0.0 wants users to explicitly use the .name_repair argument to handle non-unique or missing column names. It's probably fine unless they fully defunct this function.
Expected behavior
Complete the process without warning.