Is your feature request related to a problem? Please describe.
I want to use the templates/generic_cell_clustering.ipynb on data from the cell classification model. @ngreenwald mentioned that I should run the SOM clustering without 99.9 percentile normalization on this data, but the function train_cell_som and the downstream class CellSOMCluster do not allow me to turn off normalization.
Describe the solution you'd like
Add a flag to cluster_helpers.CellSOMCluster to the init called normalize with default True and add control flow to the init to make self.train_data = self.normalize_data(self.train_data) optional.
Add a flag to cell_som_clustering.train_cell_som called normalize with default True and provide this argument to cluster_helpers.CellSOMCluster.
Is your feature request related to a problem? Please describe. I want to use the templates/generic_cell_clustering.ipynb on data from the cell classification model. @ngreenwald mentioned that I should run the SOM clustering without 99.9 percentile normalization on this data, but the function
train_cell_som
and the downstream classCellSOMCluster
do not allow me to turn off normalization.Describe the solution you'd like Add a flag to cluster_helpers.CellSOMCluster to the init called
normalize
with defaultTrue
and add control flow to the init to makeself.train_data = self.normalize_data(self.train_data)
optional.Add a flag to cell_som_clustering.train_cell_som called
normalize
with defaultTrue
and provide this argument tocluster_helpers.CellSOMCluster
.Describe alternatives you've considered None
Additional context None