dash_plotly_QC_scRNA.py

# Dash app to visualize scRNA-seq data quality control metrics from scanpy objects
# Shoutout to Coding-with-Adam for the initial template of the project: 
# https://github.com/Coding-with-Adam/Dash-by-Plotly/blob/master/Dash%20Components/Graph/dash-graph.py

import dash
from dash import dcc, html, Output, Input
import plotly.express as px
import dash_callback_chain
import yaml
import polars as pl
pl.enable_string_cache(False)

# Set custom resolution for plots:
config_fig = {
  'toImageButtonOptions': {
    'format': 'svg',
    'filename': 'custom_image',
    'height': 600,
    'width': 700,
    'scale': 1,
  }
}

config_path = "./app/azure/config.yaml"

# Add the read-in data from the yaml file
def read_config(filename):
    with open(filename, 'r') as yaml_file:
        config = yaml.safe_load(yaml_file)
    return config

config = read_config(config_path)
path_parquet = config.get("path_parquet")
conditions = config.get("conditions")
col_features = config.get("col_features")
col_counts = config.get("col_counts")
col_mt = config.get("col_mt")

# Import the data from one .parquet file
df = pl.read_parquet(path_parquet)
#df = df.rename({"__index_level_0__": "Unnamed: 0"})

# Setup the app
external_stylesheets = ['https://codepen.io/chriddyp/pen/bWLwgP.css']
app = dash.Dash(__name__, external_stylesheets=external_stylesheets, requests_pathname_prefix='/dashboard1/')

min_value = df[col_features].min()
max_value = df[col_features].max()

min_value_2 = df[col_counts].min()
min_value_2 = round(min_value_2)
max_value_2 = df[col_counts].max()
max_value_2 = round(max_value_2)

min_value_3 = df[col_mt].min()
min_value_3 = round(min_value_3, 1)
max_value_3 = df[col_mt].max()
max_value_3 = round(max_value_3, 1)

# Loads in the conditions specified in the yaml file

# Note: Future version perhaps all values from a column in the dataframe of the parquet file
# Note 2: This could also be a tsv of the categories and own specified colors

# Create the first tab content
# Add Sliders for three QC params: N genes by counts, total amount of reads and pct MT reads

tab1_content = html.Div([
    dcc.Dropdown(id='dpdn2', value=conditions, multi=True,
                 options=conditions),
    html.Label("N Genes by Counts"),
    dcc.RangeSlider(
        id='range-slider-1',
        step=250,
        value=[min_value, max_value],
        marks={i: str(i) for i in range(min_value, max_value + 1, 250)},
    ),
    dcc.Input(id='min-slider-1', type='number', value=min_value, debounce=True),
    dcc.Input(id='max-slider-1', type='number', value=max_value, debounce=True),
    html.Label("Total Counts"),
    dcc.RangeSlider(
        id='range-slider-2',
        step=7500,
        value=[min_value_2, max_value_2],
        marks={i: str(i) for i in range(min_value_2, max_value_2 + 1, 7500)},
    ),
    dcc.Input(id='min-slider-2', type='number', value=min_value_2, debounce=True),
    dcc.Input(id='max-slider-2', type='number', value=max_value_2, debounce=True),
    html.Label("Percent Mitochondrial Genes"),
    dcc.RangeSlider(
        id='range-slider-3',
        step=0.1,
        min=0,
        max=1,
        value=[min_value_3, max_value_3],
    ),
    dcc.Input(id='min-slider-3', type='number', value=min_value_3, debounce=True),
    dcc.Input(id='max-slider-3', type='number', value=max_value_3, debounce=True),
    html.Div([
        dcc.Graph(id='pie-graph', figure={}, className='four columns',config=config_fig),
        dcc.Graph(id='my-graph', figure={}, clickData=None, hoverData=None,
                  className='four columns',config=config_fig
                  ),
        dcc.Graph(id='scatter-plot', figure={}, className='four columns',config=config_fig)
    ]),
    html.Div([
        dcc.Graph(id='scatter-plot-2', figure={}, className='four columns',config=config_fig)
    ]),
    html.Div([
        dcc.Graph(id='scatter-plot-3', figure={}, className='four columns',config=config_fig)
    ]),
    html.Div([
        dcc.Graph(id='scatter-plot-4', figure={}, className='four columns',config=config_fig)
    ]),
])

# Create the second tab content with scatter-plot-5 and scatter-plot-6
tab2_content = html.Div([
    html.Div([
            html.Label("S-cycle genes"),
            dcc.Dropdown(id='dpdn3', value="Cdc45", multi=False,
                 options=[
    "Cdc45",
    "Uhrf1",
    "Mcm2",
    "Slbp",
    "Mcm5",
    "Pola1",
    "Gmnn",
    "Cdc6",
    "Rrm2",
    "Atad2",
    "Dscc1",
    "Mcm4",
    "Chaf1b",
    "Rfc2",
    "Msh2",
    "Fen1",
    "Hells",
    "Prim1",
    "Tyms",
    "Mcm6",
    "Wdr76",
    "Rad51",
    "Pcna",
    "Ccne2",
    "Casp8ap2",
    "Usp1",
    "Nasp",
    "Rpa2",
    "Ung",
    "Rad51ap1",
    "Blm",
    "Pold3",
    "Rrm1",
    "Cenpu",
    "Gins2",
    "Tipin",
    "Brip1",
    "Dtl",
    "Exo1",
    "Ubr7",
    "Clspn",
    "E2f8",
    "Cdca7"
]),
            html.Label("G2M-cycle genes"),
            dcc.Dropdown(id='dpdn4', value="Top2a", multi=False,
                 options=[
    "Ube2c",
    "Lbr",
    "Ctcf",
    "Cdc20",
    "Cbx5",
    "Kif11",
    "Anp32e",
    "Birc5",
    "Cdk1",
    "Tmpo",
    "Hmmr",
    "Pimreg",
    "Aurkb",
    "Top2a",
    "Gtse1",
    "Rangap1",
    "Cdca3",
    "Ndc80",
    "Kif20b",
    "Cenpf",
    "Nek2",
    "Nuf2",
    "Nusap1",
    "Bub1",
    "Tpx2",
    "Aurka",
    "Ect2",
    "Cks1b",
    "Kif2c",
    "Cdca8",
    "Cenpa",
    "Mki67",
    "Ccnb2",
    "Kif23",
    "Smc4",
    "G2e3",
    "Tubb4b",
    "Anln",
    "Tacc3",
    "Dlgap5",
    "Ckap2",
    "Ncapd2",
    "Ttk",
    "Ckap5",
    "Cdc25c",
    "Hjurp",
    "Cenpe",
    "Ckap2l",
    "Cdca2",
    "Hmgb2",
    "Cks2",
    "Psrc1",
    "Gas2l3"
]),
    ]),
    html.Div([
        dcc.Graph(id='scatter-plot-5', figure={}, className='three columns',config=config_fig)
    ]),
    html.Div([
        dcc.Graph(id='scatter-plot-6', figure={}, className='three columns',config=config_fig)
    ]),
    html.Div([
        dcc.Graph(id='scatter-plot-7', figure={}, className='three columns',config=config_fig)
    ]),
    html.Div([
        dcc.Graph(id='scatter-plot-8', figure={}, className='three columns',config=config_fig)
    ]),
])

# Create the second tab content with scatter-plot-5 and scatter-plot-6
tab3_content = html.Div([
    html.Div([
            html.Label("UMAP condition 1"),
            dcc.Dropdown(id='dpdn5', value="total_counts", multi=False,
                 options=df.columns),
            html.Label("UMAP condition 2"),
            dcc.Dropdown(id='dpdn6', value="n_genes_by_counts", multi=False,
                 options=df.columns),
    ]),
    html.Div([
        dcc.Graph(id='scatter-plot-9', figure={}, className='four columns',config=config_fig)
    ]),
    html.Div([
        dcc.Graph(id='scatter-plot-10', figure={}, className='four columns',config=config_fig)
    ]),
    html.Div([
        dcc.Graph(id='scatter-plot-11', figure={}, className='four columns',config=config_fig)
    ]),
    html.Div([
            dcc.Graph(id='my-graph2', figure={}, clickData=None, hoverData=None,
                  className='four columns',config=config_fig
                  )
    ]),
])

# Define the tabs layout
app.layout = html.Div([
    dcc.Tabs(id='tabs', style= {'width': 400,
        'font-size': '100%',
        'height': 50}, value='tab1',children=[
        dcc.Tab(label='QC', value='tab1', children=tab1_content),
        dcc.Tab(label='Cell cycle', value='tab2', children=tab2_content),
        dcc.Tab(label='Custom', value='tab3', children=tab3_content),
    ]),
])

# Define the circular callback
@app.callback(
    Output("min-slider-1", "value"),
    Output("max-slider-1", "value"),
    Output("min-slider-2", "value"),
    Output("max-slider-2", "value"),
    Output("min-slider-3", "value"),
    Output("max-slider-3", "value"),
    Input("min-slider-1", "value"),
    Input("max-slider-1", "value"),
    Input("min-slider-2", "value"),
    Input("max-slider-2", "value"),
    Input("min-slider-3", "value"),
    Input("max-slider-3", "value"),
)
def circular_callback(min_1, max_1, min_2, max_2, min_3, max_3):
    return min_1, max_1, min_2, max_2, min_3, max_3

@app.callback(
    Output('range-slider-1', 'value'),
    Output('range-slider-2', 'value'),
    Output('range-slider-3', 'value'),
    Input('min-slider-1', 'value'),
    Input('max-slider-1', 'value'),
    Input('min-slider-2', 'value'),
    Input('max-slider-2', 'value'),
    Input('min-slider-3', 'value'),
    Input('max-slider-3', 'value'),
)
def update_slider_values(min_1, max_1, min_2, max_2, min_3, max_3):
    return [min_1, max_1], [min_2, max_2], [min_3, max_3]

@app.callback(
    Output(component_id='my-graph', component_property='figure'),
    Output(component_id='pie-graph', component_property='figure'),
    Output(component_id='scatter-plot', component_property='figure'),
    Output(component_id='scatter-plot-2', component_property='figure'),
    Output(component_id='scatter-plot-3', component_property='figure'),
    Output(component_id='scatter-plot-4', component_property='figure'),  # Add this new scatter plot
    Output(component_id='scatter-plot-5', component_property='figure'),
    Output(component_id='scatter-plot-6', component_property='figure'),
    Output(component_id='scatter-plot-7', component_property='figure'),
    Output(component_id='scatter-plot-8', component_property='figure'),
    Output(component_id='scatter-plot-9', component_property='figure'),
    Output(component_id='scatter-plot-10', component_property='figure'),
    Output(component_id='scatter-plot-11', component_property='figure'),
    Output(component_id='my-graph2', component_property='figure'),
    Input(component_id='dpdn2', component_property='value'),
    Input(component_id='dpdn3', component_property='value'),
    Input(component_id='dpdn4', component_property='value'),
    Input(component_id='dpdn5', component_property='value'),
    Input(component_id='dpdn6', component_property='value'),
    Input(component_id='range-slider-1', component_property='value'),
    Input(component_id='range-slider-2', component_property='value'),
    Input(component_id='range-slider-3', component_property='value')
)

def update_graph_and_pie_chart(batch_chosen, s_chosen, g2m_chosen, condition1_chosen, condition2_chosen, range_value_1, range_value_2, range_value_3):
    dff = df.filter(
        (pl.col('batch').cast(str).is_in(batch_chosen)) &
        (pl.col(col_features) >= range_value_1[0]) &
        (pl.col(col_features) <= range_value_1[1]) &
        (pl.col(col_counts) >= range_value_2[0]) &
        (pl.col(col_counts) <= range_value_2[1]) &
        (pl.col(col_mt) >= range_value_3[0]) &
        (pl.col(col_mt) <= range_value_3[1])
)
    
    #Drop categories that are not in the filtered data
    dff = dff.with_columns(dff['batch'].cast(str))
    dff = dff.with_columns(dff['batch'].cast(pl.Categorical))

    # Plot figures
    fig_violin = px.violin(data_frame=dff, x='batch', y=col_features, box=True, points="all",
                            color='batch', hover_name='batch',template="seaborn")

    # Calculate the percentage of each category (normalized_count) for pie chart
    category_counts = dff.group_by("batch").agg(pl.col("batch").count().alias("count"))
    total_count = len(dff)
    category_counts = category_counts.with_columns((pl.col("count") / total_count * 100).alias("normalized_count"))

# Display the result
    labels = category_counts["batch"].to_list()
    values = category_counts["normalized_count"].to_list()

    total_cells = total_count  # Calculate total number of cells
    pie_title = f'Percentage of Total Cells: {total_cells}'  # Include total cells in the title

    fig_pie = px.pie(names=labels, values=values, title=pie_title,template="seaborn")

    # Create the scatter plots
    fig_scatter = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color='batch',
                             labels={'X_umap-0': 'umap1' , 'X_umap-1': 'umap2'},
                             hover_name='batch',template="seaborn")

    fig_scatter_2 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color=col_mt,
                             labels={'X_umap-0': 'umap1' , 'X_umap-1': 'umap2'},
                             hover_name='batch',template="seaborn")

    fig_scatter_3 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color=col_features,
                             labels={'X_umap-0': 'umap1' , 'X_umap-1': 'umap2'},
                             hover_name='batch',template="seaborn")


    fig_scatter_4 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color=col_counts,
                             labels={'X_umap-0': 'umap1' , 'X_umap-1': 'umap2'},
                             hover_name='batch',template="seaborn")
    
    fig_scatter_5 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color=s_chosen,
                            labels={'X_umap-0': 'umap1' , 'X_umap-1': 'umap2'},
                            hover_name='batch', title="S-cycle gene:",template="seaborn")

    fig_scatter_6 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color=g2m_chosen,
                            labels={'X_umap-0': 'umap1' , 'X_umap-1': 'umap2'},
                            hover_name='batch', title="G2M-cycle gene:",template="seaborn")
    
    fig_scatter_7 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color="S_score",
                            labels={'X_umap-0': 'umap1' , 'X_umap-1': 'umap2'},
                            hover_name='batch', title="S score:",template="seaborn")
    
    fig_scatter_8 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color="G2M_score",
                            labels={'X_umap-0': 'umap1' , 'X_umap-1': 'umap2'},
                            hover_name='batch', title="G2M score:",template="seaborn")
    
    fig_scatter_9 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color=condition1_chosen,
                            labels={'X_umap-0': 'umap1' , 'X_umap-1': 'umap2'},
                            hover_name='batch',template="seaborn")
    
    fig_scatter_10 = px.scatter(data_frame=dff, x='X_umap-0', y='X_umap-1', color=condition2_chosen,
                            labels={'X_umap-0': 'umap1' , 'X_umap-1': 'umap2'},
                            hover_name='batch',template="seaborn")
    
    fig_scatter_11 = px.scatter(data_frame=dff, x=condition1_chosen, y=condition2_chosen, color='batch',
                            #labels={'X_umap-0': 'umap1' , 'X_umap-1': 'umap2'},
                            hover_name='batch',template="seaborn")
    
    fig_violin2 = px.violin(data_frame=dff, x=condition1_chosen, y=condition2_chosen, box=True, points="all",
                            color=condition1_chosen, hover_name=condition1_chosen,template="seaborn")


    return fig_violin, fig_pie, fig_scatter, fig_scatter_2, fig_scatter_3, fig_scatter_4, fig_scatter_5, fig_scatter_6, fig_scatter_7, fig_scatter_8, fig_scatter_9, fig_scatter_10, fig_scatter_11, fig_violin2

# Set http://localhost:5000/ in web browser
# Now create your regular FASTAPI application

if __name__ == '__main__':
    app.run_server(debug=True, use_reloader=False) #host='0.0.0.0', #, port=5000