SAHA SCIMAP

This repository contains the protein annotation scripts for the SAHA project.

SCIMAPPrep.ipynb

Doesn't do much to be honest.

RunSciMap.py

This python script runs the SCIMAP package to conduct gating and hierarchically assign cell types.

Before running the script, change line 41

newAD = sm.pp.rescale(newAD,imageid='SAHA_name', method='by_image')

And line 48

newAD.obs.groupby('SAHA_name').phenotype.value_counts()

Replace 'SAHA_name' with the obs column you use to separate the batches.

Run the script like so:

python RunSciMap.py adata.h5ad workflow_broad.csv adataSM.h5ad

DifExpr.ipynb

This script examines how many cells are assigned differently between MaxFuse and SCIMAP and examines for cells in on annotation how they are assigned in another annotation.

SCIMAPCompare.ipynb

This script examines visually how cell typing differences betwen MaxFuse and SCIMAP.

PrettyPictures.ipynb

This script generates the spatial mapping of cell typing derived from SCIMAP.

UMAP_TSNE.ipynb

This script generates the UMAP, TSNE, and the cell proportion plots.