Parkinson’s disease in the spinal cord: an exploratory study to establish T2*w, MTR and diffusion-weighted imaging metric values

import plotly.express as px
from plotly.offline import plot
from IPython.core.display import HTML
import plotly.graph_objects as go
from plotly.subplots import make_subplots
import pandas as pd
import base64
import plotly.io as pio
pio.renderers.default = "plotly_mimetype"

# Load the data
df = pd.read_csv('../../data/parkinsons-spinalcord-mri-metrics/data/participants.csv')

# Add a column for age groups (35-39, 40-44, etc.)
age_group_labels_list = ['35-39', '40-44', '45-49', '50-54', '55-59', '60-64', '65-69', '70-74', '75-79', '80-84']
df['age_groups'] = pd.cut(df['age'], bins=[35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85], labels=age_group_labels_list)

# Create a list to specify the order of the UPDRSIII groups
UPDRS_group_labels_list = ['CTRL', 'early', 'mid', 'adv']
UPDRS_group_labels_ticks = ['HC', 'Early PD', 'Mid PD', 'Adv PD'] # Add custom text for plotting

# Divide the data based on if the modality was used for each subject ('Y' = yes, 'N' = no)
df_DWI = df[df['DWI'] == 'Y']
df_MTR = df[df['MTR'] == 'Y']
df_T2star = df[df['T2star'] == 'Y']

# Create subplots: 1 row, 2 columns
fig = make_subplots(rows=2, cols=2, row_heights=[0.75, 0.25], column_widths=[0.5, 0.5],)

# Figure dimensions
fig.update_layout(width=760, height=798)

# Load static background image (in the "templates_for_figures" folder) and encode as base64
with open("../templates_for_figures/figure1_template.png", "rb") as image_file:
    encoded_image = base64.b64encode(image_file.read()).decode()

### ADD STATIC BACKGROUND IMAGE ###
fig.update_layout(
    images=[dict(
        source="data:image/png;base64," + encoded_image,
        x=-0.155,
        y=1.11,
        xanchor="left",
        yanchor="top",
        sizex=1.23,
        sizey=4.5, 
        layer="below",  
    )],
)

### SUBPLOT 1 ###

# Add histogram for DWI
fig.add_trace(go.Histogram(
    x=df_DWI['age_groups'], 
    name='DWI', 
    marker=dict(color='#1C5F82'),
    showlegend=True,
    legendgroup='DWI',
    ),
    row=2, col=1
)

# Add histogram for MTR
fig.add_trace(go.Histogram(
    x=df_MTR['age_groups'], 
    name='MTR', 
    marker=dict(color='black'),
    showlegend=True,
    legendgroup='MTR',
    ), 
    row=2, col=1
)

# Add histogram for T2star
fig.add_trace(go.Histogram(
    x=df_T2star['age_groups'], 
    name='T2*w', 
    marker=dict(color='#D1D1D1'),
    showlegend=True,
    legendgroup='T2*w',
    ), 
    row=2, col=1
)

### SUBPLOT 2 ###

# Add histogram for DWI
fig.add_trace(go.Histogram(
    x=df_DWI['UPDRSIII_group'], 
    name='DWI', 
    marker=dict(color='#1C5F82'),
    showlegend=False,
    legendgroup='DWI',
    ),
    row=2, col=2
)

# Add histogram for MTR
fig.add_trace(go.Histogram(
    x=df_MTR['UPDRSIII_group'], 
    name='MTR', 
    marker=dict(color='black'),
    showlegend=False,
    legendgroup='MTR',
    ), 
    row=2, col=2
)

# Add histogram for T2star
fig.add_trace(go.Histogram(
    x=df_T2star['UPDRSIII_group'], 
    name='T2*w', 
    marker=dict(color='#D1D1D1'),
    showlegend=False,
    legendgroup='T2*w',
    ), 
    row=2, col=2
)

fig.update_layout(
    font=dict(family='Arial', size=12, color='black'), 
    legend=dict(
        orientation="h", 
        yanchor="bottom", 
        y=0.25, 
        xanchor="center",  
        x=0.5
    ),
    plot_bgcolor='white',
)

# Update axis properties for each subplot
fig.update_xaxes(
    title="Age",
    categoryorder="array", 
    categoryarray=age_group_labels_list,  
    tickangle=-45,
    gridwidth=0.5,
    row=2, col=1 
)

fig.update_xaxes(
    title="Subject Categories",
    categoryorder="array",
    categoryarray=UPDRS_group_labels_list, 
    tickvals=list(range(len(UPDRS_group_labels_list))),  # Specify tick positions
    ticktext=list(UPDRS_group_labels_ticks),  # Provide custom text for each tick
    tickangle=0,
    gridwidth=0.5,
    row=2, col=2  
)

fig.update_yaxes(
    title="Number of subjects",
    showgrid=True,  
    gridcolor='lightgray', 
    gridwidth=0.5,
    row=2, col=1  
)

fig.update_yaxes( 
    title="Number of subjects",
    showgrid=True,  
    gridcolor='lightgray',
    gridwidth=0.5,
    row=2, col=2  
)

fig.show()