search

broadinstitute / lincs-cell-painting

Processed Cell Painting Data for the LINCS Drug Repurposing Project
BSD 3-Clause "New" or "Revised" License
25 stars 13 forks source link

Spherized data UMAP figures #64

Closed gwaybio closed 3 years ago

gwaybio commented 3 years ago

In #63 I add spherized profiles for batch 1 and batch 2 LINCS data. Here is a birds-eye view of what the profiles look like:

Summary

It is hard to determine from this view exactly how much the profile quality has improved. The DMSO profiles are still distributed widely in the UMAP space, but many compounds form distinct islands. It also doesn't look too much different (at least by a cursory glance) to be too much different from a non-spherized (level 4 profiles) LINCS dataset (see here).

Batch 2 profiles are potentially more interesting. We see distinct islands separated by cell type! This is expected, but also quite exciting. I do not have UMAP coordinates with level 4 profiles.

Batch 1

lincs_whole_plate_spherized_batch1

Batch 2

lincs_whole_plate_spherized_batch2

lincs_whole_plate_spherized_batch2_cell_line

gwaybio commented 3 years ago

Also note that spherized profiles using level 4 data normalized by DMSO (instead of whole plate) did not perform well in UMAP (either b/c this spherized strategy didn't work well, or b/c UMAP didn't handle these data well)

lincs_dmso_spherized_batch1

gwaybio commented 3 years ago

closed in favor of the figures available at https://github.com/broadinstitute/lincs-cell-painting/tree/master/spherized_profiles