app.py

import gradio as gr
import flowio
import matplotlib.pyplot as plt
import io
import pandas as pd

# Function to parse FCS file and extract data and metadata
def parse_fcs(file):
    # Use flowio to parse the FCS file
    fcs_data = flowio.FlowData(file.name)

    # Extract channel names and data
    channel_names = [channel['PnN'] for channel in fcs_data.channels]
    data = pd.DataFrame(fcs_data.events, columns=channel_names)

    return data, channel_names

# Function to plot the data based on selected x and y parameters
def plot_dot(file, x_param, y_param):
    if not file:
        return "Please upload an FCS file."

    try:
        data, columns = parse_fcs(file)

        if x_param not in columns or y_param not in columns:
            return "Invalid parameters selected. Please choose valid parameters from the dropdown."

        # Create the plot
        plt.figure(figsize=(8, 6))
        plt.scatter(data[x_param], data[y_param], s=1, alpha=0.5, color="blue")
        plt.xlabel(x_param)
        plt.ylabel(y_param)
        plt.title("Flow Cytometry Dot Plot")
        plt.grid(True)

        # Save plot to a BytesIO object
        buf = io.BytesIO()
        plt.savefig(buf, format="png")
        buf.seek(0)
        plt.close()

        # Save the plot as a temporary file for display
        temp_file = "/tmp/dot_plot.png"
        with open(temp_file, "wb") as f:
            f.write(buf.getbuffer())
        return temp_file
    except Exception as e:
        return f"Error: {e}"

# Function to dynamically update parameter options after file upload
def get_parameters(file):
    if not file:
        return [], []

    try:
        _, columns = parse_fcs(file)
        return gr.Dropdown.update(choices=columns), gr.Dropdown.update(choices=columns)
    except Exception as e:
        return [f"Error: {e}"], [f"Error: {e}"]

# Create Gradio interface
with gr.Blocks() as app:
    gr.Markdown("# Flow Cytometry Dot Plot Viewer")

    with gr.Row():
        fcs_file = gr.File(label="Upload FCS File")

    with gr.Row():
        x_param = gr.Dropdown(label="X Parameter", choices=[], interactive=True)
        y_param = gr.Dropdown(label="Y Parameter", choices=[], interactive=True)

    plot_btn = gr.Button("Generate Plot")
    plot_output = gr.Image(type="filepath", label="Dot Plot")

    # Update parameter dropdowns on file upload
    fcs_file.change(get_parameters, inputs=[fcs_file], outputs=[x_param, y_param])

    # Generate plot on button click
    plot_btn.click(plot_dot, inputs=[fcs_file, x_param, y_param], outputs=plot_output)

# Run the app
app.launch()