app.py

import gradio as gr
import pandas as pd
import numpy as np
import umap
import json
import matplotlib.pyplot as plt
import os
import scanpy as sc
import subprocess
import sys
from io import BytesIO
from sklearn.linear_model import LogisticRegression
from huggingface_hub import hf_hub_download


def load_and_predict_with_classifier(x, model_path, output_path, save):

    # Load the model parameters from the JSON file
    with open(model_path, 'r') as f:
        model_params = json.load(f)

    # Reconstruct the logistic regression model
    model_loaded = LogisticRegression(multi_class='multinomial', solver='lbfgs', max_iter=1000)
    model_loaded.coef_ = np.array(model_params["coef"])
    model_loaded.intercept_ = np.array(model_params["intercept"])
    model_loaded.classes_ = np.array(model_params["classes"])

    # output predictions
    y_pred = model_loaded.predict(x)

    # Convert the array to a Pandas DataFrame
    if save:
        df = pd.DataFrame(y_pred, columns=["predicted_cell_type"])
        df.to_csv(output_path, index=False, header=False)
    
    return y_pred


def plot_umap(adata):

    labels = pd.Categorical(adata.obs["cell_type"])

    reducer = umap.UMAP(n_neighbors=15, min_dist=0.1, n_components=2, random_state=42)
    embedding = reducer.fit_transform(adata.obsm["X_uce"])

    plt.figure(figsize=(10, 8))

    # Create the scatter plot
    scatter = plt.scatter(embedding[:, 0], embedding[:, 1], c=labels.codes, cmap='Set1', s=50, alpha=0.6)

    # Create a legend
    handles = []
    for i, cell_type in enumerate(labels.categories):
        handles.append(plt.Line2D([0], [0], marker='o', color='w', label=cell_type,
                                  markerfacecolor=plt.cm.Set1(i / len(labels.categories)), markersize=10))

    plt.legend(handles=handles, title='Cell Type')
    plt.title('UMAP projection of the data')
    plt.xlabel('UMAP1')
    plt.ylabel('UMAP2')
    
    # Save plot to a BytesIO object
    buf = BytesIO()
    plt.savefig(buf, format='png')
    buf.seek(0)
    
    # Read the image from BytesIO object
    img = plt.imread(buf, format='png')

    return img


def toggle_file_input(default_dataset):
    if default_dataset != "None":
        return gr.update(interactive=False)  # Disable the file input if a default dataset is selected
    else:
        return gr.update(interactive=True)  # Enable the file input if no default dataset is selected


def main(input_file_path, species, default_dataset):

    # Get the current working directory
    current_working_directory = os.getcwd()
    
    # Print the current working directory
    print("Current Working Directory:", current_working_directory)

    # clone and cd into UCE repo
    os.system('git clone https://github.com/minwoosun/UCE.git')
    os.chdir('/home/user/app/UCE')

    # Get the current working directory
    current_working_directory = os.getcwd()
    
    # Print the current working directory
    print("Current Working Directory:", current_working_directory)

    # Specify the path to the directory you want to add
    new_directory = "/home/user/app/UCE"
    
    # Add the directory to the Python path
    sys.path.append(new_directory)

    # Set default dataset path
    default_dataset_1_path = hf_hub_download(repo_id="minwoosun/uce-misc", filename="100_pbmcs_proc_subset.h5ad")
    default_dataset_2_path = hf_hub_download(repo_id="minwoosun/uce-misc", filename="1k_pbmcs_proc_subset.h5ad")

    # If the user selects a default dataset, use that instead of the uploaded file
    if default_dataset == "PBMC 100 cells":
        input_file_path = default_dataset_1_path
    elif default_dataset == "PBMC 1000 cells":
        input_file_path = default_dataset_2_path

    ##############
    #     UCE    #
    ##############
    from evaluate import AnndataProcessor
    from accelerate import Accelerator

    dir_path = '/home/user/app/UCE/'
    model_loc = 'minwoosun/uce-100m'

    print(input_file_path)
    print(dir_path)
    print(model_loc)
    
    # Construct the command
    command = [
        'python', 
        '/home/user/app/UCE/eval_single_anndata.py', 
        '--adata_path', input_file_path, 
        '--dir', dir_path, 
        '--model_loc', model_loc
    ]
    
    # Print the command for debugging
    print("Running command:", command)

    print("---> RUNNING UCE")
    result = subprocess.run(command, capture_output=True, text=True, check=True)
    print(result.stdout)
    print(result.stderr)
    print("---> FINSIH UCE")

    ################################
    #   Cell-type classification   #
    ################################

    # Set output file path
    file_name_with_ext = os.path.basename(input_file_path)
    file_name = os.path.splitext(file_name_with_ext)[0]
    pred_file = "/home/user/app/UCE/" + f"{file_name}_predictions.csv"
    model_path = hf_hub_download(repo_id="minwoosun/uce-misc", filename="tabula_sapiens_v1_logistic_regression_model_weights.json")

    file_name_with_ext = os.path.basename(input_file_path)
    file_name = os.path.splitext(file_name_with_ext)[0]
    output_file = "/home/user/app/UCE/" + f"{file_name}_uce_adata.h5ad"
    adata = sc.read_h5ad(output_file)
    x = adata.obsm['X_uce']

    y_pred = load_and_predict_with_classifier(x, model_path, pred_file, save=True)
    
    ##############
    #    UMAP    #
    ##############
    img = plot_umap(adata)
  
    return img, output_file, pred_file


if __name__ == "__main__":   

    with gr.Blocks() as demo:
        gr.Markdown(
            '''
            <div style="text-align:center; margin-bottom:20px;">
                <span style="font-size:3em; font-weight:bold;">UCE 100M Demo 🦠</span>
            </div>
            <div style="text-align:center; margin-bottom:10px;">
                <span style="font-size:1.5em; font-weight:bold;">Universal Cell Embeddings: Zero-Shot Cell-Type Classification in Action!</span>
            </div>
            <div style="text-align:center; margin-bottom:20px;">
                <a href="https://github.com/minwoosun/UCE">
                    <img src="https://badges.aleen42.com/src/github.svg" alt="GitHub" style="display:inline-block; margin-right:10px;">
                </a>
                <a href="https://www.biorxiv.org/content/10.1101/2023.11.28.568918v1">
                    <img src="https://img.shields.io/badge/bioRxiv-2023.11.28.568918-green?style=plastic" alt="Paper" style="display:inline-block; margin-right:10px;">
                </a>
                <a href="https://colab.research.google.com/drive/1opud0BVWr76IM8UnGgTomVggui_xC4p0?usp=sharing">
                    <img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab" style="display:inline-block; margin-right:10px;">
                </a>
            </div>
            <div style="text-align:left; margin-bottom:20px;">
                Upload a `.h5ad` single cell gene expression file and select the species (Human/Mouse). 
                The demo will generate UMAP projections of the embeddings and allow you to download the embeddings for further analysis.
            </div>
            <div style="margin-bottom:20px;">
                <ol style="list-style:none; padding-left:0;">
                    <li>1. Upload your `.h5ad` file or select one of the default datasets (subset of 10x pbmc data)</li>
                    <li>2. Select the species</li>
                    <li>3. Click "Run" to view the UMAP scatter plot</li>
                    <li>4. Download the UCE embeddings and predicted cell-types</li>
                </ol>
            </div>
            <div style="text-align:left; line-height:1.8;">
                Please consider citing the following paper if you use this tool in your research:
            </div>
            <div style="text-align:left; line-height:1.8;">
                Rosen, Y., Roohani, Y., Agarwal, A., Samotorčan, L., Tabula Sapiens Consortium, Quake, S. R., & Leskovec, J. Universal Cell Embeddings: A Foundation Model for Cell Biology. bioRxiv. https://doi.org/10.1101/2023.11.28.568918
            </div>
            '''
        )

        # Define Gradio inputs and outputs
        file_input = gr.File(label="Upload a .h5ad single cell gene expression file or select a default dataset below")
        # species_input = gr.Dropdown(choices=["human", "mouse"], label="Select species")
        with gr.Row():
            species_input = gr.Dropdown(choices=["human", "mouse"], label="Select species")
            default_dataset_input = gr.Dropdown(choices=["None", "PBMC 100 cells", "PBMC 1000 cells"], label="Select default dataset")

        # Attach the `change` event to the dropdown
        default_dataset_input.change(
            toggle_file_input,
            inputs=[default_dataset_input],
            outputs=[file_input]
        )

        run_button = gr.Button("Run", elem_classes="run-button")
        
        # Arrange UMAP plot and file output side by side
        with gr.Row():
            image_output = gr.Image(type="numpy", label="UMAP of UCE Embeddings")
            file_output = gr.File(label="Download embeddings")
            pred_output = gr.File(label="Download predictions")
    
        # Add the components and link to the function
        run_button.click(
            fn=main, 
            inputs=[file_input, species_input, default_dataset_input], 
            outputs=[image_output, file_output, pred_output]
        )

        examples = gr.Examples(
        	examples = [[None, "human", "PBMC 100 cells"],[None, "human", "PBMC 1000 cells"]],
        	inputs = [file_input, species_input, default_dataset_input],
        	cache_examples=True
        )

    demo.launch()