How to change genomewideline_value of volcano plot with Range Slider

Question

I'm trying to make a volcano plot and I want to change genomewideline_value based on Range Slider value but it not worked. Below is my sample code:

import pandas as pd
import dash
from dash.dependencies import Input, Output
import dash_bio as dashbio
from dash import html, dcc

app = dash.Dash(__name__)
df = pd.read_csv('https://git.io/volcano_data1.csv')
app.layout = html.Div([
    'Effect sizes',
    dcc.RangeSlider(
        id='default-volcanoplot-input',
        min=-3,
        max=3,
        step=0.05,
        marks={i: {'label': str(i)} for i in range(-3, 3)},
        value=[-0.5, 1]
    ),
    dcc.RangeSlider(
        id='default-volcanoplot-input-2',
        min=-3,
        max=3,
        step=0.05,
        marks={j: {'label': str(j)} for j in range(-3, 3)},
        value=[0.5]
    ),    
    html.Br(),
    html.Div(
        dcc.Graph(
            id='dashbio-default-volcanoplot',
            figure={}
            )
        )
])

@app.callback(
    Output('dashbio-default-volcanoplot', 'figure'),
    [Input('default-volcanoplot-input', 'value'),
    Input('default-volcanoplot-input-2', 'value')]
)
def update_volcanoplot(effects,effects_2):
    return dashbio.VolcanoPlot(
        dataframe=df,
        effect_size='EFFECTSIZE', 
        logp=True,
        p='P', 
        snp=None,
        gene='GENE',
        genomewideline_value=effects_2,
        genomewideline_width = 1,
        effect_size_line=effects,
        effect_size_line_width = 1,
        xlabel='log2 Fold Change', 
        ylabel='-(p-adjusted)')

if __name__ == '__main__':
    app.run_server(debug=False)

When running this code, it has error that said: ValueError: ('Lengths must match to compare', (9934,), (1,))

If I change genomewideline_value=effects_2 to genomewideline_value=0.5it worked well but I cannot change it by slider.

What should I do in this case. Thank you.

Answer 1

I don't use occasional or Dash, but I think what I noticed when I ran your code is that genomewideline_value only accepts a single value instead of taking a range value. if I change it from a range slider to a drop down, the change is as intended. I have tested this in the Colab environment with the jupyter_dash module in place, so please modify it for your environment.

import pandas as pd
import dash
from dash.dependencies import Input, Output
import dash_bio as dashbio
from dash import html, dcc

#app = dash.Dash(__name__)
app = JupyterDash(__name__)

df = pd.read_csv('https://git.io/volcano_data1.csv')
#print(df)

app.layout = html.Div([
    'Effect sizes',
    dcc.RangeSlider(
        id='default-volcanoplot-input',
        min=-3,
        max=3,
        step=0.05,
        marks={i: {'label': str(i)} for i in range(-3, 3)},
        value=[-0.5, 1]
    ),
    dcc.Dropdown(id='volcanpplot_dp',
                 options=[0,1,2,3,4,5,6,7,8],
                 value=4        
    ),
    html.Br(),
    html.Div(
        dcc.Graph(
            id='dashbio-default-volcanoplot',
            figure=dashbio.VolcanoPlot(
                dataframe=df
            )
        )
    )
])

@app.callback(
    Output('dashbio-default-volcanoplot', 'figure'),
    [
     Input('default-volcanoplot-input', 'value'),
     Input('volcanpplot_dp', 'value')
     ]
)
def update_volcanoplot(effects, effects2):
    return dashbio.VolcanoPlot(
        dataframe=df,
        point_size=8,
        genomewideline_value=effects2,
        genomewideline_width=2,
        effect_size_line=effects,
        effect_size_line_width=2,
    )

if __name__ == '__main__':
    app.run_server(debug=True, mode='inline')