dash_bio.ManhattanPlot Examples and Reference

see ManhattanPlot in action.

ManhattanPlot

An example of a default ManhattanPlot component without any extra properties.

Threshold value 

import pandas as pd
from dash import Dash, html, dcc, Input, Output, callback
import dash_bio as dashbio

app = Dash(__name__)

df = pd.read_csv('https://git.io/manhattan_data.csv')

app.layout = html.Div([
    'Threshold value',
    dcc.Slider(
        id='default-manhattanplot-input',
        min=1,
        max=10,
        marks={
            i: {'label': str(i)} for i in range(10)
        },
        value=6
    ),
    html.Br(),
    html.Div(
        dcc.Graph(
            id='default-dashbio-manhattanplot',
            figure=dashbio.ManhattanPlot(
                dataframe=df
            )
        )
    )
])

@callback(
    Output('default-dashbio-manhattanplot', 'figure'),
    Input('default-manhattanplot-input', 'value')
)
def update_manhattanplot(threshold):

    return dashbio.ManhattanPlot(
        dataframe=df,
        genomewideline_value=threshold
    )

if __name__ == '__main__':
    app.run(debug=True)

Customization

Line Colors

Change the colors of the suggestive line and the genome-wide line.

import pandas as pd
from dash import dcc
import dash_bio as dashbio

df = pd.read_csv('https://git.io/manhattan_data.csv')

n_chr = 23  # number of chromosome pairs in humans
assert 'CHR' in df.columns
assert df['CHR'].max() == n_chr

# Trim down the data
DATASET = df.groupby('CHR').apply(lambda u: u.head(50))
DATASET = DATASET.droplevel('CHR').reset_index(drop=True)

manhattanplot = dashbio.ManhattanPlot(
    dataframe=DATASET,
    suggestiveline_color='#AA00AA',
    genomewideline_color='#AA5500'
)

dcc.Graph(figure=manhattanplot)

Highlighted Points Color

Change the color of the points that are considered significant.

import pandas as pd
from dash import dcc
import dash_bio as dashbio

df = pd.read_csv('https://git.io/manhattan_data.csv')

n_chr = 23  # number of chromosome pairs in humans
assert 'CHR' in df.columns
assert df['CHR'].max() == n_chr

# Trim down the data
DATASET = df.groupby('CHR').apply(lambda u: u.head(50))
DATASET = DATASET.droplevel('CHR').reset_index(drop=True)

manhattanplot = dashbio.ManhattanPlot(
    dataframe=DATASET,
    highlight_color='#00FFAA'
)

dcc.Graph(figure=manhattanplot)

ManhattanPlot Properties

Access this documentation in your Python terminal with:
```python

help(dash_bio.ManhattanPlot)
```

Our recommended IDE for writing Dash apps is Dash Enterprise’s
Data Science Workspaces,
which has typeahead support for Dash Component Properties.
Find out if your company is using
Dash Enterprise.

dataframe (dataframe; required): A pandas dataframe which must contain at
least the following three columns:
- the chromosome number
- genomic base-pair position
- a numeric quantity to plot such as a p-value or zscore

chrm (string; default 'CHR'): A string denoting the column name for
the chromosome. This column must be float or integer. Minimum
number of chromosomes required is 1. If you have X, Y, or MT
chromosomes, be sure to renumber these 23, 24, 25, etc.

bp (string; default 'BP'): A string denoting the column name for the
chromosomal position.

p (string; default 'P'): A string denoting the column name for the
float quantity to be plotted on the y-axis. This column must be
numeric. It does not have to be a p-value. It can be any numeric
quantity such as peak heights, Bayes factors, test statistics. If
it is not a p-value, make sure to set logp = False.

snp (string; default 'SNP'): A string denoting the column name for
the SNP names (e.g., rs number). More generally, this column could
be anything that identifies each point being plotted. For example,
in an Epigenomewide association study (EWAS), this could be the
probe name or cg number. This column should be a character. This
argument is optional, however it is necessary to specify it if you
want to highlight points on the plot, using the highlight argument
in the figure method.

gene (string; default 'GENE'): A string denoting the column name for
the GENE names. This column could be a string or a float. More
generally, it could be any annotation information that you want
to include in the plot.

annotation (string; optional): A string denoting the column to use
as annotations. This column could be a string or a float. It
could be any annotation information that you want to include in
the plot (e.g., zscore, effect size, minor allele frequency).

logp (bool; optional): If True, the -log10 of the p-value is
plotted. It isn’t very useful to plot raw p-values; however,
plotting the raw value could be useful for other genome-wide plots
(e.g., peak heights, Bayes factors, test statistics, other
“scores”, etc.)

title (string; default 'Manhattan Plot'): The title of the graph.

showgrid (bool; default true): Boolean indicating whether gridlines
should be shown.

xlabel (string; optional): Label of the x axis.

ylabel (string; default '-log10(p)'): Label of the y axis.

point_size (number; default 5): Size of the points of the Scatter
plot.

showlegend (bool; default true): Boolean indicating whether legends
should be shown.

col (string; optional): A string representing the color of the
points of the scatter plot. Can be in any color format accepted by
plotly.graph_objects.

suggestiveline_value (bool | float; default 8): A value which must
be either False to deactivate the option, or a numerical value
corresponding to the p-value at which the line should be drawn.
The line has no influence on the data points.

suggestiveline_color (string; default 'grey'): Color of the suggestive
line.

suggestiveline_width (number; default 2): Width of the suggestive
line.

genomewideline_value (bool | float; default -log10(5e-8)): A boolean
which must be either False to deactivate the option, or a numerical value
corresponding to the p-value above which the data points are
considered significant.

genomewideline_color (string; default 'red'): Color of the genome-wide
line. Can be in any color format accepted by plotly.graph_objects.

genomewideline_width (number; default 1): Width of the genome-wide
line.

highlight (bool; default True): turning on/off the highlighting of
data points considered significant.

highlight_color (string; default 'red'): Color of the data points
highlighted because they are significant. Can be in any color
format accepted by plotly.graph_objects.

# ...
Example 1: Random Manhattan Plot
'''
dataframe = pd.DataFrame(
    np.random.randint(0,100,size=(100, 3)),
    columns=['P', 'CHR', 'BP'])
fig = create_manhattan(dataframe, title='XYZ Manhattan plot')

plotly.offline.plot(fig, image='png')
'''

Example Data