Usage

This section provides a minimal example of displaying a clustered matrix with Celldega.

Clustergram parquet_data

The Clustergram widget accepts a parquet_data argument that contains the network encoded as Parquet tables. Using this approach avoids transferring large JSON structures to the browser. You can obtain this dictionary from a Matrix instance using Matrix.export_viz_parquet().

import celldega as dega
import pandas as pd

# Load expression data
df = pd.read_parquet("df_sig.parquet")

# Create and cluster the matrix
mat = dega.clust.Matrix(df, name="demo")
mat.clust()

# Export to Parquet-encoded bytes
pq_data = mat.export_viz_parquet()

# Initialize widget with parquet_data
cgm = dega.viz.Clustergram(parquet_data=pq_data, width=500, height=500)
cgm

Clustergram can also be initialized directly from a Matrix instance which internally uses export_viz_parquet. Passing a legacy JSON network is now deprecated.