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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() |