gsMap3D 0.1.0a1__py3-none-any.whl

gsMap/utils/manhattan_plot.py

@@ -0,0 +1,643 @@
+"""
+Modified from dash-bio ManhattanPlot (https://github.com/plotly/dash-bio/blob/master/dash_bio/component_factory/_manhattan.py)
+"""
+
+import warnings
+
+import numpy as np
+import pandas as pd
+import plotly.graph_objects as go
+from pandas.api.types import is_numeric_dtype
+
+# %%
+SUGGESTIVE_LINE_LABEL = "suggestive line"
+GENOMEWIDE_LINE_LABEL = "genomewide line"
+
+
+def _get_hover_text(df, snpname=None, genename=None, annotationname=None):
+    """Format the hover text used in Manhattan and Volcano plots.
+    :param (dataFrame) df: A pandas dataframe.
+    :param (string) snpname: 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.
+    :param (string) genename: A string denoting the column name for the
+    GENE names.
+    :param (string) annotationname: A string denoting the column name for
+    annotations. This could be any annotation information that you
+    want to include in the plot (e.g., zscore, effect size, minor allele
+    frequency).
+    """
+    hover_text = ""
+    if snpname is not None and snpname in df.columns:
+        hover_text = "SNP: " + df[snpname].astype(str)
+
+    if genename is not None and genename in df.columns:
+        hover_text = hover_text + "<br>GENE: " + df[genename].astype(str)
+
+    if annotationname is not None and annotationname in df.columns:
+        hover_text = hover_text + "<br>" + df[annotationname].astype(str)
+
+    return hover_text
+
+
+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_color="red",
+    highlight_gene_list=None,
+    highlight=True,
+    **kwargs,
+):
+    """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,
+        color_by=kwargs.get('highlight_color_by')
+    )
+
+    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,
+        highlight_gene_list=highlight_gene_list,
+    )
+
+
+class _ManhattanPlot:
+    def __init__(
+        self, x, chrm="CHR", bp="BP", p="P", snp="SNP", gene="GENE", annotation=None, logp=True, color_by=None
+    ):
+        """
+        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]
+
+        if color_by is not None:
+            if color_by in x.columns:
+                self.data[color_by] = x[color_by]
+            else:
+                 import logging
+                 logging.getLogger(__name__).warning(f"color_by column {color_by} not found in input.")
+
+        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"
+
+        self.data[self.index] = 0  # Initialize with zeros as default value
+
+        if not self.data.empty and len(self.data[chrm].unique()) > 0:
+            idx = 0
+            for i in self.data[chrm].unique():
+                idx = idx + 1
+                self.data.loc[self.data[chrm] == i, self.index] = int(idx)
+        else:
+            import logging
+
+            logger = logging.getLogger("gsMap.utils.manhattan_plot")
+            logger.warning(
+                "No chromosome data found or empty dataframe when creating Manhattan plot"
+            )
+
+        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]) / 2.0) + 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) / 2.0) + 1)
+
+            self.xlabel = "Chromosome"
+            self.data[self.pos] = self.data[self.pos].astype(self.data[bp].dtype)
+
+            if self.nChr > 10:  # To avoid crowded labels
+                self.ticksLabels = [
+                    t
+                    if np.mod(int(t), 2)  # Only every two ticks
+                    else ""
+                    for t in 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",
+        highlight_gene_list=None,
+        highlight_color_by=None,
+    ):
+        """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.
+        - highlight_color_by (string; optional): A column name in the
+        dataframe to use for coloring the highlighted points (gradient).
+
+        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
+        highlight_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 highlight_gene_list:
+                    raise KeyError("Please provide a list of genes to highlight")
+                common_genes = set(self.data[self.geneName].unique()).intersection(
+                    highlight_gene_list
+                )
+                if len(common_genes) == 0:
+                    # Don't raise error, just warn
+                    import logging
+                    logging.getLogger(__name__).warning("No common genes found in the data to highlight")
+                elif len(common_genes) < len(highlight_gene_list):
+                    warnings.warn(
+                        f"Some genes don't contain any SNP to highlight: "
+                        f": {set(highlight_gene_list) - common_genes}",
+                        stacklevel=2,
+                    )
+
+                highlight_tmp = self.data[self.data[self.geneName].isin(common_genes)]
+
+                highlight_hover_text = _get_hover_text(
+                    highlight_tmp,
+                    snpname=self.snpName,
+                    genename=self.geneName,
+                    annotationname=self.annotationName,
+                )
+
+        # Remove the highlighted data from the DataFrame if not empty
+        if highlight_tmp.empty:
+            data = self.data
+        else:
+            data = self.data.drop(highlight_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,
+                    name="chr%i" % data[self.chrName].unique()[0],
+                    marker={"color": col[0], "size": point_size},
+                    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()  # Get chromosome name
+
+                hover_text = _get_hover_text(
+                    tmp,
+                    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="Chr%i" % chromo[0],
+                        marker={"color": col[icol], "size": point_size},
+                        text=hover_text,
+                    )
+                )
+
+                icol = icol + 1
+
+        if not highlight_tmp.empty:
+            if highlight_color_by and highlight_color_by in highlight_tmp.columns:
+                marker_dict = dict(
+                    color=highlight_tmp[highlight_color_by].values,
+                    colorscale="Plasma",
+                    showscale=True,
+                    colorbar=dict(title=highlight_color_by, x=1.1, len=0.5),
+                    size=point_size * 2,
+                )
+            else:
+                marker_dict = dict(
+                    color=highlight_color,
+                    size=point_size * 2,
+                )
+
+            data_to_plot.append(
+                go.Scattergl(
+                    x=highlight_tmp[self.pos].values,
+                    y=-np.log10(highlight_tmp[self.pName].values)
+                    if self.logp
+                    else highlight_tmp[self.pName].values,
+                    mode="markers",
+                    text=highlight_hover_text,
+                    marker=marker_dict,
+                    name="SNP-Gene Pairs of interest",
+                )
+            )
+
+        layout.shapes = horizontallines
+
+        return go.Figure(data=data_to_plot, layout=layout)