Description
Question
Dear @AnnaChristina and ncem developers,
thank you for creating this impressive tool! I am studying immune signalling in the visium data. For this reason, I deconvoluted a single cell reference atlas into the visium anndata and created anndatas containing the cell specific expression as shown here: https://github.com/theislab/ncem_benchmarks/blob/main/notebooks/data_preparation/deconvolution/cell2location_human_lymphnode.ipynb.
I did not find any further explanation in the documentation or the tutorials and could not figure it by looking into the functions available but am I correct to analyze the visium signaling like this eg.
## Initialize ncem model for deconvoluted Visium
ncem_ip = InterpreterDeconvolution()
ncem_ip.data = customLoaderDeconvolution(
adata=adata, patient=None, library_id='library_id', radius=None
)
print("Load the data for visium")
get_data_custom(interpreter=ncem_ip, deconvolution=True)
print("Get sender and receiver effects")
ncem_ip.get_sender_receiver_effects()
## Get type coupling
type_coupling = ncem_ip.type_coupling_analysis_circular(edge_width_scale=0.3,edge_attr='magnitude', figsize=(20,20), text_space=1.28, de_genes_threshold=150,suffix=f"{niche}_type_coupling_analysis_circular.pdf")
type_coupling.to_csv(f."/#{sample}_T_ST_{niche}_NCEM_Object_type_coupling.csv")
## Get type coupling
ncem_ip.type_coupling_analysis(figsize=(15, 15),suffix=f"{niche}_type_coupling_analysis_Heatmap.pdf")
or should I first train the estimator and then load the model into the interpreter.
Either way, how can I access, or plot features learned by the estimator for deconvoluted visium?
Thanks in advance for your help!