Quick Start Guide

This tutorial will get you started with FADVI in just a few minutes.

Installation

First, install FADVI:

pip install fadvi

Basic Usage

  1. Import libraries

import fadvi
import scanpy as sc

  1. Load data

# Load your data
adata = sc.read_h5ad("your_data.h5ad")

  1. Initialize and train the model

 fadvi.FADVI.setup_anndata(adata,
    batch_key="batch",
    labels_key="cell_type",
    unlabeled_category="Unknown",
    layer="counts"
)

# Create FADVI model
model = fadvi.FADVI(adata)

# Train the model
model.train(max_epochs=30)

  1. Get results

# Get latent representation
latent = model.get_latent_representation()
adata.obsm["X_fadvi_l"] = latent

Next Steps