scmoib-package

To do list ( & open questions)

• add notebooks directly to the github account while dev? in its own folder

metrics

• can we easily plot the mean weighted distance and the node count could be plotted as a umap.

• can we make some kind histogram/distribution plot for teh weighted distance ?

• can we check if the silhouette score has to be on the PCA space all the time or can it work on the knn o

• can we easily plot the mean weighted distance and the node count could be plotted as a umap.

• can we make some kind histogram/distribution plot for teh weighted distance ?

• can we check if the silhouette score has to be on the PCA space all the time or can it work on the knn orkey_added=None, copy=False, something ? (general question )

• make the functions that are part the class directly available (then they return values)

• adjust the plotting functions based on how we save the metrics.

• Anna fix your weird graoh UMAP !

• add annotations to each functions.

• clean the metrics_stuff (maybe put it in tools as util or a subdirectory) it's up to atai

package

• requirements ?
• unit test ? (I vote against it because I am lazy)
• let's setup the automated checks on github like Kris did for episcanpy @Anna
• refine umap_barcodes (got critical errors from pycharm)