search

lmcinnes / umap

Uniform Manifold Approximation and Projection
BSD 3-Clause "New" or "Revised" License
7.44k stars 808 forks source link

distance matrix and labels on it #434

Open aspitaleri opened 4 years ago

aspitaleri commented 4 years ago

Hi there and congrats for the nice tool! I am using UMAP reduction to clusterize my own custom distance matrix (using metric='precomputed') and as suggested here https://umap-learn.readthedocs.io/en/latest/clustering.html#umap-enhanced-clustering I applied HDBSCAN too to clusterize the results. Actually, the cluster analysis directly from UMAP is alreayd good but I'd like to get the info from each cloud points. Is there any way to achieve this without passing through HDBSCAN? Best

jc-healy commented 4 years ago

Hi there,

Have a look at umap.plot.interactive() ( https://umap-learn.readthedocs.io/en/latest/plotting.html). It should allow you to pass in a data frame of labels along with you UMAP model and have those labels be displayed when you hover your mouse over the points in the plot. This should allow you to quickly and easily see what each cloud of points was representing.

On Wed, May 20, 2020 at 11:24 AM Andrea Spitaleri notifications@github.com wrote:

Hi there and congrats for the nice tool! I am using UMAP reduction to clusterize my own custom distance matrix (using metric='precomputed') and as suggested here https://umap-learn.readthedocs.io/en/latest/clustering.html#umap-enhanced-clustering I applied HDBSCAN too to clusterize the results. Actually, the cluster analysis directly from UMAP is alreayd good but I'd like to get the info from each cloud points. Is there any way to achieve this without passing through HDBSCAN? Best

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/lmcinnes/umap/issues/434, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC3IUWXTZ5UA7CSUEU53CETRSPY3DANCNFSM4NGBD22A .

aspitaleri commented 4 years ago

Hi @jc-healy thanks for the reply. Actually I have a lot points to see, so I was something like to get the coordinate of the plot in order to assign them in downstream analysis such as a dataframe: UMAP1 UMAP2 Label is there any way to extract the coordinates from the plot?

aspitaleri commented 4 years ago

Sorry ... it was easier than I thought

169