Update app.py

app.py

@@ -1,86 +1,45 @@
 import gradio as gr
-import flowio
-import matplotlib.pyplot as plt
-import io
 import pandas as pd
+import matplotlib.pyplot as plt
+import fcsparser
 
-# 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 empty dropdown updates if no file is uploaded
-        return gr.Dropdown.update(choices=[]), gr.Dropdown.update(choices=[])
-
-    try:
-        _, columns = parse_fcs(file)
-        return gr.Dropdown.update(choices=columns), gr.Dropdown.update(choices=columns)
-    except Exception as e:
-        # Log the error and return empty dropdowns
-        print(f"Error parsing FCS file: {e}")
-        return gr.Dropdown.update(choices=[], value=None), gr.Dropdown.update(choices=[], value=None)
-
-# 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", file_types=[".fcs"])
-
-    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()
+    # Parse the FCS file
+    meta, data = fcsparser.parse(file.name)
+    return pd.DataFrame(data)
+
+def plot_fcs(data, x_axis, y_axis):
+    # Plot the data
+    plt.figure(figsize=(10, 6))
+    plt.scatter(data[x_axis], data[y_axis], alpha=0.5)
+    plt.xlabel(x_axis)
+    plt.ylabel(y_axis)
+    plt.title(f"{x_axis} vs {y_axis}")
+    return plt
+
+def process_fcs(file):
+    # Parse the FCS file and get the DataFrame
+    df = parse_fcs(file)
+    
+    # Get the column names for x and y axis choices
+    columns = df.columns.tolist()
+    
+    # Create a Gradio interface for selecting x and y axis
+    with gr.Blocks() as demo:
+        with gr.Row():
+            x_axis = gr.Dropdown(choices=columns, label="Select X-axis")
+            y_axis = gr.Dropdown(choices=columns, label="Select Y-axis")
+        plot = gr.Plot()
+        
+        # Update the plot when the dropdowns change
+        x_axis.change(plot_fcs, inputs=[gr.State(df), x_axis, y_axis], outputs=plot)
+        y_axis.change(plot_fcs, inputs=[gr.State(df), x_axis, y_axis], outputs=plot)
+    
+    return demo
+
+# Gradio interface for uploading the FCS file
+with gr.Blocks() as demo:
+    file = gr.File(label="Upload FCS File", file_types=[".fcs"])
+    output = gr.Interface(fn=process_fcs, inputs=file, outputs="component", live=True)
+
+demo.launch()