Pca before umap

1. Do you need to do PCA before UMAP?
2. Why is UMAP after PCA?
3. Is UMAP the same as PCA?
4. What is better than UMAP?

Do you need to do PCA before UMAP?

Prior to doing t-SNE or UMAP, Seurat's vignettes recommend doing PCA to perform an initial reduction in the dimensionality of the input dataset while still preserving most of the important data structure.

Why is UMAP after PCA?

UMAP outperformed t-SNE and PCA, if we look at the 2d and 3d plot, we can see mini-clusters that are being separated well. It is very effective for visualizing clusters or groups of data points and their relative proximities.

Is UMAP the same as PCA?

While UMAP is clearly slower than PCA, its scaling performance is dramatically better than MulticoreTSNE, and for even larger datasets the difference is only going to grow. This concludes our look at scaling by dataset size.

What is better than UMAP?

Ivis outperforms UMAP at preserving global structure and should be considered for many applications of dimensionality reduction.