Interactive Manhattan plot with string chromosome names

Question

I'm trying to generate ManhattanPlot using Dash-plotly library for python: https://dash.plotly.com/dash-bio/manhattanplot

I have SNP results data for plants like wheat which have chromosome names with letters e.g. 3A, 3B, 3D.

Is is possible to handle such identifiers (with letter suffixes) in plotly/python?

In the documentation there is the following remark about chromosome id:

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.

I have data for many plant genomes which contain letters in chromosome names. It seems that CHR column can't have string values which is strange from the user perspective.

Answer 1

This looks like an unfortunate case where the developer of the dashbio.ManhattanPlot object made an assumption about the chrm parameter.

Looking through _manhattan.py in the dash-bio repository, you can start by commenting out these lines so that the CHRM column isn't required to be numerical.

EDIT: the other changes were updating self.ticksLabels to be strings instead of integers, and increasing the threshold from 10 to 20 ticks when deciding when to display every other ticklabel instead of all ticklabels. I've included my local version of _manhattan.py file below:

from __future__ import absolute_import

import numpy as np
import pandas as pd
from pandas.api.types import is_numeric_dtype

import plotly.graph_objects as go

from .utils import _get_hover_text

SUGGESTIVE_LINE_LABEL = "suggestive line"
GENOMEWIDE_LINE_LABEL = "genomewide line"


def ManhattanPlot(
        dataframe,
        chrm="CHR",
        bp="BP",
        p="P",
        snp="SNP",
        gene="GENE",
        annotation=None,
        logp=True,
        title="Manhattan Plot",
        showgrid=True,
        xlabel=None,
        ylabel='-log10(p)',
        point_size=5,
        showlegend=True,
        col=None,
        suggestiveline_value=-np.log10(1e-8),
        suggestiveline_color='#636efa',
        suggestiveline_width=1,
        genomewideline_value=-np.log10(5e-8),
        genomewideline_color='#EF553B',
        genomewideline_width=1,
        highlight=True,
        highlight_color="red",
):
    """Returns a figure for a manhattan plot.

Keyword arguments:
- 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')
    '''

    """

    mh = _ManhattanPlot(
        dataframe,
        chrm=chrm,
        bp=bp,
        p=p,
        snp=snp,
        gene=gene,
        annotation=annotation,
        logp=logp
    )

    return mh.figure(
        title=title,
        showgrid=showgrid,
        xlabel=xlabel,
        ylabel=ylabel,
        point_size=point_size,
        showlegend=showlegend,
        col=col,
        suggestiveline_value=suggestiveline_value,
        suggestiveline_color=suggestiveline_color,
        suggestiveline_width=suggestiveline_width,
        genomewideline_value=genomewideline_value,
        genomewideline_color=genomewideline_color,
        genomewideline_width=genomewideline_width,
        highlight=highlight,
        highlight_color=highlight_color
    )


class _ManhattanPlot():

    def __init__(
            self,
            x,
            chrm="CHR",
            bp="BP",
            p="P",
            snp="SNP",
            gene="GENE",
            annotation=None,
            logp=True
    ):
        """
        Keyword arguments:
        - 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. This 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 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 name for
        an annotation. This column could be a string or a float.  This
        could be any annotation information that you want to include in
        the plot (e.g. zscore, effect size, minor allele frequency).
        - logp (bool; default True): 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.).

        Returns:
        - A ManhattanPlot object."""

        # checking the validity of the arguments

        # Make sure you have chrm, bp and p columns and that they are of
        # numeric type
        if chrm not in x.columns.values:
            raise KeyError("Column %s not found in 'x' data.frame" % chrm)
        # else:
        #     if not is_numeric_dtype(x[chrm].dtype):
        #         raise TypeError("%s column should be numeric. Do you have "
        #                         "'X', 'Y', 'MT', etc? If so change to "
        #                         "numbers and try again." % chrm)

        if bp not in x.columns.values:
            raise KeyError("Column %s not found in 'x' data.frame" % bp)
        else:
            if not is_numeric_dtype(x[bp].dtype):
                raise TypeError("%s column should be numeric type" % bp)

        if p not in x.columns.values:
            raise KeyError("Column %s not found in 'x' data.frame" % p)
        else:
            if not is_numeric_dtype(x[p].dtype):
                raise TypeError("%s column should be numeric type" % p)

        # Create a new DataFrame with columns named after chrm, bp, and p.
        self.data = pd.DataFrame(data=x[[chrm, bp, p]])

        if snp is not None:
            if snp not in x.columns.values:
                # Warn if you don't have a snp column
                raise KeyError(
                    "snp argument specified as %s but column not found in "
                    "'x' data.frame" % snp)
            else:
                # If the input DataFrame has a snp column, add it to the new
                # DataFrame
                self.data[snp] = x[snp]

        if gene is not None:
            if gene not in x.columns.values:
                # Warn if you don't have a gene column
                raise KeyError(
                    "gene argument specified as %s but column not found in "
                    "'x' data.frame" % gene)
            else:
                # If the input DataFrame has a gene column, add it to the new
                # DataFrame
                self.data[gene] = x[gene]

        if annotation is not None:
            if annotation not in x.columns.values:
                # Warn if you don't have an annotation column
                raise KeyError(
                    "annotation argument specified as %s but column not "
                    "found in 'x' data.frame" % annotation
                )
            else:
                # If the input DataFrame has a gene column, add it to the new
                # DataFrame
                self.data[annotation] = x[annotation]

        self.xlabel = ""
        self.ticks = []
        self.ticksLabels = []
        self.nChr = len(x[chrm].unique())
        self.chrName = chrm
        self.pName = p
        self.snpName = snp
        self.geneName = gene
        self.annotationName = annotation
        self.logp = logp

        # Set positions, ticks, and labels for plotting

        self.index = 'INDEX'
        self.pos = 'POSITION'

        # Fixes the bug where one chromosome is missing by adding a sequential
        # index column.
        idx = 0
        for i in self.data[chrm].unique():
            idx = idx + 1
            self.data.loc[self.data[chrm] == i, self.index] = int(idx)
        # Set the type to be the same as provided for chrm column
        self.data[self.index] = \
            self.data[self.index].astype(self.data[chrm].dtype)

        # This section sets up positions and ticks. Ticks should be placed in
        # the middle of a chromosome. The new pos column is added that keeps
        # a running sum of the positions of each successive chromosome.
        # For example:
        # chrm bp pos
        # 1   1  1
        # 1   2  2
        # 2   1  3
        # 2   2  4
        # 3   1  5

        if self.nChr == 1:
            # For a single chromosome
            self.data[self.pos] = self.data[bp]
            self.ticks.append(int(len(self.data[self.pos]) / 2.) + 1)
            self.xlabel = "Chromosome %s position" % (self.data[chrm].unique())
            self.ticksLabels = self.ticks
        else:
            # For multiple chromosomes
            lastbase = 0
            for i in self.data[self.index].unique():
                if i == 1:
                    self.data.loc[self.data[self.index] == i, self.pos] = \
                        self.data.loc[self.data[self.index] == i, bp].values
                else:
                    prevbp = self.data.loc[self.data[self.index] == i - 1, bp]
                    # Shift the basepair position by the largest bp of the
                    # current chromosome
                    lastbase = lastbase + prevbp.iat[-1]

                    self.data.loc[self.data[self.index] == i, self.pos] = \
                        self.data.loc[self.data[self.index] == i, bp].values \
                        + lastbase

                tmin = min(self.data.loc[self.data[self.index] == i, self.pos])
                tmax = max(self.data.loc[self.data[self.index] == i, self.pos])
                self.ticks.append(int((tmin + tmax) / 2.) + 1)

            self.xlabel = 'Chromosome'
            self.data[self.pos] = self.data[self.pos].astype(
                self.data[bp].dtype)

            if self.nChr > 20:  # To avoid crowded labels
                self.ticksLabels = [
                    chrm if np.mod(int(t+1), 2)  # Only every two ticks
                    else ''
                    for t,chrm in enumerate(self.data[chrm].unique())
                ]
            else:
                self.ticksLabels = self.data[chrm].unique()  # All the ticks

    def figure(
            self,
            title="Manhattan Plot",
            showgrid=True,
            xlabel=None,
            ylabel='-log10(p)',
            point_size=5,
            showlegend=True,
            col=None,
            suggestiveline_value=-np.log10(1e-8),
            suggestiveline_color='blue',
            suggestiveline_width=1,
            genomewideline_value=-np.log10(5e-8),
            genomewideline_color='red',
            genomewideline_width=1,
            highlight=True,
            highlight_color="red",
    ):
        """Keyword arguments:
    - 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): Whether to turn on or 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.

    Returns:
    - A figure formatted for plotly.graph_objects.

        """

        xmin = min(self.data[self.pos].values)
        xmax = max(self.data[self.pos].values)

        horizontallines = []

        if suggestiveline_value:
            suggestiveline = go.layout.Shape(
                name=SUGGESTIVE_LINE_LABEL,
                type="line",
                fillcolor=suggestiveline_color,
                line=dict(
                    color=suggestiveline_color,
                    width=suggestiveline_width
                ),
                x0=xmin, x1=xmax, xref="x",
                y0=suggestiveline_value, y1=suggestiveline_value, yref="y"
            )
            horizontallines.append(suggestiveline)

        if genomewideline_value:
            genomewideline = go.layout.Shape(
                name=GENOMEWIDE_LINE_LABEL,
                type="line",
                fillcolor=genomewideline_color,
                line=dict(
                    color=genomewideline_color,
                    width=genomewideline_width
                ),
                x0=xmin, x1=xmax, xref="x",
                y0=genomewideline_value, y1=genomewideline_value, yref="y"
            )
            horizontallines.append(genomewideline)

        data_to_plot = []  # To contain the data traces
        tmp = pd.DataFrame()  # Empty DataFrame to contain the highlighted data

        if highlight:
            if not isinstance(highlight, bool):
                if self.snpName not in self.data.columns.values:
                    raise KeyError(
                        "snp argument specified for highlight as %s but "
                        "column not found in the data.frame" % self.snpName
                    )
            else:
                if not genomewideline_value:
                    raise Warning(
                        "The genomewideline_value you entered is not a "
                        "positive value, or False, you cannot set highlight "
                        "to True in that case.")
                tmp = self.data

                # Sort the p-values (or -log10(p-values) above the line
                if genomewideline_value:
                    if self.logp:
                        tmp = tmp.loc[-np.log10(tmp[self.pName])
                                      > genomewideline_value]
                    else:
                        tmp = tmp.loc[tmp[self.pName] > genomewideline_value]

                highlight_hover_text = _get_hover_text(
                    tmp,
                    snpname=self.snpName,
                    genename=self.geneName,
                    annotationname=self.annotationName
                )

                if not tmp.empty:
                    data_to_plot.append(
                        go.Scattergl(
                            x=tmp[self.pos].values,
                            y=-np.log10(tmp[self.pName].values) if self.logp
                            else tmp[self.pName].values,
                            mode="markers",
                            text=highlight_hover_text,
                            marker=dict(
                                color=highlight_color,
                                size=point_size
                            ),
                            name="Point(s) of interest"
                        )
                    )

        # Remove the highlighted data from the DataFrame if not empty
        if tmp.empty:
            data = self.data
        else:
            data = self.data.drop(self.data.index[tmp.index])

        if self.nChr == 1:

            if col is None:
                col = ['black']

            # If single chromosome, ticks and labels automatic.
            layout = go.Layout(
                title=title,
                xaxis={
                    'title': self.xlabel if xlabel is None else xlabel,
                    'showgrid': showgrid,
                    'range': [xmin, xmax],
                },
                yaxis={'title': ylabel},
                hovermode='closest'
            )

            hover_text = _get_hover_text(
                data,
                snpname=self.snpName,
                genename=self.geneName,
                annotationname=self.annotationName
            )

            data_to_plot.append(
                go.Scattergl(
                    x=data[self.pos].values,
                    y=-np.log10(data[self.pName].values) if self.logp
                    else data[self.pName].values,
                    mode="markers",
                    showlegend=showlegend,
                    marker={
                        'color': col[0],
                        'size': point_size,
                        'name': "chr%i" % data[self.chrName].unique()
                    },
                    text=hover_text
                )
            )
        else:
            # if multiple chrms, use the ticks and labels you created above.
            layout = go.Layout(
                title=title,
                xaxis={
                    'title': self.xlabel if xlabel is None else xlabel,
                    'showgrid': showgrid,
                    'range': [xmin, xmax],
                    'tickmode': "array",
                    'tickvals': self.ticks,
                    'ticktext': self.ticksLabels,
                    'ticks': "outside"
                },
                yaxis={'title': ylabel},
                hovermode='closest'
            )

            icol = 0
            if col is None:
                col = [
                    'black' if np.mod(i, 2)
                    else 'grey' for i in range(self.nChr)
                ]

            for i in data[self.index].unique():

                tmp = data[data[self.index] == i]
                
                chromo = tmp[self.chrName].unique()[0]  # Get chromosome name

                hover_text = _get_hover_text(
                    data,
                    snpname=self.snpName,
                    genename=self.geneName,
                    annotationname=self.annotationName
                )

                data_to_plot.append(
                    go.Scattergl(
                        x=tmp[self.pos].values,
                        y=-np.log10(tmp[self.pName].values) if self.logp
                        else tmp[self.pName].values,
                        mode="markers",
                        showlegend=showlegend,
                        name=f"Chr{chromo}",
                        marker={
                            'color': col[icol],
                            'size': point_size
                        },
                        text=hover_text
                    )
                )

                icol = icol + 1

        layout.shapes = horizontallines

        return go.Figure(data=data_to_plot, layout=layout)

Then, I modified the plotly-dash example here to use a modified df where the "CHR" column has string values like "1A","1B",..."9A","9B" instead of integers, and tested that the Dash app renders these strings correctly.

import numpy as np
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/manhattan_data.csv')

## create some sample data where "CHR" column
## contains strings of the format "{number}{letter}" 
## where {letter} is one of "A","B"

np.random.seed(42)
df_test = df[df["CHR"] < 10].copy()
for _, df_group in df_test.groupby("CHR"):
    start, end = df_group.index[0], df_group.index[-1]
    midpt = (start + end) // 2
    df_test['CHR'].loc[start:midpt] = df_group['CHR'].loc[start:midpt].astype(str) + 'A'
    df_test['CHR'].loc[midpt:end] = df_group['CHR'].loc[midpt:end].astype(str) + 'B'

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_test
            )
        )
    )
])

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

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

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