The pathogen-embed command accepts a --random-seed argument that is supposed to pass through to all functions that rely on random seeds. We pass this random seed to the t-SNE and UMAP constructors, but we don't pass the value to the PCA or MDS constructors even though both of PCA and MDS accept a random_state keyword argument.
We should update the logic for those embedding methods to include the random state from the random seed argument.
The
pathogen-embedcommand accepts a--random-seedargument that is supposed to pass through to all functions that rely on random seeds. We pass this random seed to the t-SNE and UMAP constructors, but we don't pass the value to the PCA or MDS constructors even though both of PCA and MDS accept arandom_statekeyword argument.We should update the logic for those embedding methods to include the random state from the random seed argument.