app.py

import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
from scipy.interpolate import interp1d
from shiny import render
from shiny.express import input, output, ui
from utils import (
    generate_2d_sequence,
    plot_seq_full_label
)
import os
import matplotlib as mpl
import seaborn as sns
mpl.rcParams.update(mpl.rcParamsDefault)

df_gene_varient = pd.read_parquet("gene_varient.parquet")
df_histone = pd.read_parquet("histone.parquet")
df_gene_len = len(df_gene_varient)
df_histone_len = len(df_histone)
df_enhancer_annotation = pd.read_parquet('enhancer_annotation.parquet')
df_enhancer_annotation_len = len(df_enhancer_annotation)
ui.page_opts(fillable=True)

with ui.navset_card_tab(id="tab"):
    with ui.nav_panel("Gene Varient"):
        ui.panel_title("Is there a pattern to gene varient location?")
        with ui.layout_columns():
            with ui.card():
                ui.input_slider("sample", "sample", 0, df_gene_len, 40)
                
        def plot_loss_rates(df, sample, enhancer=False):
            y_values = generate_2d_sequence(df['seq'].iloc[sample])[0]
            x_values = generate_2d_sequence(df['seq'].iloc[sample])[1]
            
            integers = df['labels'].iloc[sample]
            if enhancer:
                K= 128
                res = []
                for i in integers:
                    res.extend([i]*K)
                integers = res
            # Create a DataFrame with the x values, y values, and integers
            data = {'x': x_values, 'y': y_values, 'color': integers}

            # fig, ax = plt.subplots()


            # Create a figure and axis
            fig, ax = plt.subplots()
            
            # Create the scatter plot
            scatter = ax.scatter(data['x'], data['y'], c=data['color'], cmap='tab20', s=0.5)
            
            # Add a colorbar
            cbar = fig.colorbar(scatter, ax=ax)
            cbar.set_label('Label')
            
            # Set labels and title
            # ax.set_xlabel('X')
            # ax.set_ylabel('Y')
            # ax.set_title(f"Loss ra")
            # ax.set_xlabel("Training steps")
            # ax.set_ylabel("Loss rate")
            return fig

        @render.plot()
        def plot_context_size_scaling():
            fig = plot_loss_rates(df_gene_varient,input.sample() )
            if fig:
                return fig
    with ui.nav_panel("Histone Modification"):
        ui.panel_title("Is there a pattern to histone modification?")
        with ui.layout_columns():
            with ui.card():
                ui.input_slider("sample_histone", "sample", 0, df_histone_len, 40)
        
        
        def plot_histone(df,sample):
            y_values = generate_2d_sequence(df['seq'].iloc[sample])[0]
            x_values = generate_2d_sequence(df['seq'].iloc[sample])[1]
            
            integers = str((np.argwhere(df['labels'][sample] == np.amax(df['labels'][sample]))).flatten().tolist())
            # Create a DataFrame with the x values, y values, and integers
            data = {'x': x_values, 'y': y_values, 'color': integers}

            fig, ax = plt.subplots()

            sns.scatterplot(x='x', y='y', hue='color', data=data, palette='viridis', ax=ax)
            ax.legend()
            # ax.set_title(f"Loss ra")
            # ax.set_xlabel("Training steps")
            # ax.set_ylabel("Loss rate")
            return fig      
        @render.plot()
        def plot_histones_two():
            fig = plot_histone(df_histone,input.sample_histone() )
            if fig:
                return fig
    with ui.nav_panel("Enhancer Annontations"):
        ui.panel_title("Is there a pattern to enhancer annotations?")
        with ui.layout_columns():
            with ui.card():
                ui.input_slider("sample_enhancer", "sample", 0, df_enhancer_annotation_len, 40)
        @render.plot()
        def plot_enhancer():
            fig = plot_loss_rates(df_enhancer_annotation,input.sample_enhancer() , True)
            if fig:
                return fig