Understanding outputs¶
Output directory structure¶
output/
├── input_data/
│ ├── _adata.h5ad
│ ├── celloracle_links.pkl
│ ├── communication.pkl
│ ├── LRs.parquet
├── betadata/
│ ├── PAX5_betadata.parquet
│ ├── FOXO1_betadata.parquet
│ ├── CD79A_betadata.parquet
│ ├── ...
│ ├── IL21_betadata.parquet
│ ├── IL4_betadata.parquet
│ ├── CCR4_betadata.parquet
├── logs/
│ ├── training_TIMESTAMP.log
Understanding beta coefficients¶
Here, each _betadata.parquet has shape cell x modulators. For example, the column names are labeled as ‘beta_EGR1’ for the transcription factor EGR1, ‘beta_IL21$IL21R’ for the ligand-receptor interaction between IL21 and IL21R, and ‘beta_IL27#PATZ1’ for the transcriptional association of PATZ1 and IL27.
These values represent the estimated modulatory effect of each modulator gene/gene pair on the target gene. (_betadata.parquet).index.name.
In essense, this also represents the spatially varying links between genes in the network.