gsMap 1.71.2__py3-none-any.whl → 1.72.3__py3-none-any.whl

gsMap/utils/manhattan_plot.py

@@ -1,12 +1,13 @@
-'''
+"""
 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
-from pandas.api.types import is_numeric_dtype
-
 import plotly.graph_objects as go
-import warnings
+from pandas.api.types import is_numeric_dtype
 
 # %%
 SUGGESTIVE_LINE_LABEL = "suggestive line"
@@ -31,69 +32,65 @@ def _get_hover_text(df, snpname=None, genename=None, annotationname=None):
     want to include in the plot (e.g., zscore, effect size, minor allele
     frequency).
     """
-    hover_text = ''
+    hover_text = ""
     if snpname is not None and snpname in df.columns:
-        hover_text = 'SNP: ' + df[snpname].astype(str)
+        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)
+        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)
+        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=True,
-        highlight_color="red",
-        highlight_gene_list=None,
+    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",
+    highlight_gene_list=None,
 ):
     """Returns a figure for a manhattan plot.
 
-Keyword arguments:
-- dataframe (dataframe; required): A pandas dataframe which must contain at
+    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
+    - 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
+    - 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
+    - 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
+    - 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
@@ -101,50 +98,50 @@ Keyword arguments:
     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
+    - 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
+    - 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
+    - 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
+    - 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
+    - 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
+    - showlegend (bool; default true): Boolean indicating whether legends
     should be shown.
-- col (string; optional): A string representing the color of the
+    - 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
+    - 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
+    - suggestiveline_color (string; default 'grey'): Color of the suggestive
     line.
-- genomewideline_value (bool | float; default -log10(5e-8)): A boolean
+    - 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
+    - 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
+    - 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
+    - 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.
 
@@ -160,16 +157,8 @@ Keyword arguments:
     '''
 
     """
-
     mh = _ManhattanPlot(
-        dataframe,
-        chrm=chrm,
-        bp=bp,
-        p=p,
-        snp=snp,
-        gene=gene,
-        annotation=annotation,
-        logp=logp
+        dataframe, chrm=chrm, bp=bp, p=p, snp=snp, gene=gene, annotation=annotation, logp=logp
     )
 
     return mh.figure(
@@ -188,22 +177,13 @@ Keyword arguments:
         genomewideline_width=genomewideline_width,
         highlight=highlight,
         highlight_color=highlight_color,
-        highlight_gene_list=highlight_gene_list
+        highlight_gene_list=highlight_gene_list,
     )
 
 
-class _ManhattanPlot():
-
+class _ManhattanPlot:
     def __init__(
-            self,
-            x,
-            chrm="CHR",
-            bp="BP",
-            p="P",
-            snp="SNP",
-            gene="GENE",
-            annotation=None,
-            logp=True
+        self, x, chrm="CHR", bp="BP", p="P", snp="SNP", gene="GENE", annotation=None, logp=True
     ):
         """
         Keyword arguments:
@@ -245,9 +225,10 @@ class _ManhattanPlot():
         (e.g., peak heights, Bayes factors, test statistics, other
         "scores", etc.).
 
-        Returns:
-        - A ManhattanPlot object."""
-
+        Returns
+        -------
+        - A ManhattanPlot object.
+        """
         # checking the validity of the arguments
 
         # Make sure you have chrm, bp and p columns and that they are of
@@ -256,9 +237,11 @@ class _ManhattanPlot():
             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)
+                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)
@@ -279,8 +262,8 @@ class _ManhattanPlot():
             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)
+                    "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
@@ -290,8 +273,8 @@ class _ManhattanPlot():
             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)
+                    "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
@@ -322,8 +305,8 @@ class _ManhattanPlot():
 
         # Set positions, ticks, and labels for plotting
 
-        self.index = 'INDEX'
-        self.pos = 'POSITION'
+        self.index = "INDEX"
+        self.pos = "POSITION"
 
         # Fixes the bug where one chromosome is missing by adding a sequential
         # index column.
@@ -332,8 +315,7 @@ class _ManhattanPlot():
             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)
+        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
@@ -349,7 +331,7 @@ class _ManhattanPlot():
         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.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:
@@ -357,96 +339,97 @@ class _ManhattanPlot():
             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
+                    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
+                    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.ticks.append(int((tmin + tmax) / 2.0) + 1)
 
-            self.xlabel = 'Chromosome'
-            self.data[self.pos] = self.data[self.pos].astype(
-                self.data[bp].dtype)
+            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 ''
+                    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
+        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,
     ):
         """Keyword arguments:
-    - title (string; default 'Manhattan Plot'): The title of the
+        - title (string; default 'Manhattan Plot'): The title of the
         graph.
-    - showgrid (bool; default True): Boolean indicating whether
+        - 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
+        - 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
+        - showlegend (bool; default True): Boolean indicating whether
         legends should be shown.
-    - col (string; optional): A string representing the color of the
+        - 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
+        - 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
+        - suggestiveline_color (string; default 'grey'): Color of the
         suggestive line.
-    - suggestiveline_width (number; default 2): Width of the
+        - suggestiveline_width (number; default 2): Width of the
         suggestive line.
-    - genomewideline_value (bool | float; default -log10(5e-8)): A
+        - 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
+        - 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
+        - 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
+        - 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.
+        Returns
+        -------
+        - A figure formatted for plotly.graph_objects.
 
         """
-
         xmin = min(self.data[self.pos].values)
         xmax = max(self.data[self.pos].values)
 
@@ -457,12 +440,13 @@ class _ManhattanPlot():
                 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"
+                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)
 
@@ -471,12 +455,13 @@ class _ManhattanPlot():
                 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"
+                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)
 
@@ -492,18 +477,17 @@ class _ManhattanPlot():
                     )
             else:
                 if not highlight_gene_list:
-                    raise KeyError(
-                        "Please provide a list of genes to highlight"
-                    )
-                common_genes = set(self.data[self.geneName].values).intersection(highlight_gene_list)
+                    raise KeyError("Please provide a list of genes to highlight")
+                common_genes = set(self.data[self.geneName].values).intersection(
+                    highlight_gene_list
+                )
                 if len(common_genes) == 0:
-                    raise Warning(
-                        "No common genes found in the data to highlight"
-                    )
+                    raise 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}"
+                        f": {set(highlight_gene_list) - common_genes}",
+                        stacklevel=2,
                     )
 
                 highlight_tmp = self.data
@@ -514,11 +498,9 @@ class _ManhattanPlot():
                     highlight_tmp,
                     snpname=self.snpName,
                     genename=self.geneName,
-                    annotationname=self.annotationName
+                    annotationname=self.annotationName,
                 )
 
-
-
         # Remove the highlighted data from the DataFrame if not empty
         if highlight_tmp.empty:
             data = self.data
@@ -526,42 +508,37 @@ class _ManhattanPlot():
             data = self.data.drop(self.data.index[highlight_tmp.index])
 
         if self.nChr == 1:
-
             if col is None:
-                col = ['black']
+                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],
+                    "title": self.xlabel if xlabel is None else xlabel,
+                    "showgrid": showgrid,
+                    "range": [xmin, xmax],
                 },
-                yaxis={'title': ylabel},
-                hovermode='closest'
+                yaxis={"title": ylabel},
+                hovermode="closest",
             )
 
             hover_text = _get_hover_text(
                 data,
                 snpname=self.snpName,
                 genename=self.geneName,
-                annotationname=self.annotationName
+                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,
+                    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(),
-                    marker={
-                        'color': col[0],
-                        'size': point_size
-                    },
-                    text=hover_text
+                    marker={"color": col[0], "size": point_size},
+                    text=hover_text,
                 )
             )
         else:
@@ -569,24 +546,21 @@ class _ManhattanPlot():
             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"
+                    "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'
+                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)
-                ]
+                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]
@@ -597,32 +571,31 @@ class _ManhattanPlot():
                     tmp,
                     snpname=self.snpName,
                     genename=self.geneName,
-                    annotationname=self.annotationName
+                    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,
+                        y=-np.log10(tmp[self.pName].values)
+                        if self.logp
+                        else tmp[self.pName].values,
                         mode="markers",
                         showlegend=showlegend,
                         name="Chr%i" % chromo,
-                        marker={
-                            'color': col[icol],
-                            'size': point_size
-                        },
-                        text=hover_text
+                        marker={"color": col[icol], "size": point_size},
+                        text=hover_text,
                     )
                 )
 
                 icol = icol + 1
 
-
         if not highlight_tmp.empty:
             data_to_plot.append(
                 go.Scattergl(
                     x=highlight_tmp[self.pos].values,
-                    y=-np.log10(highlight_tmp[self.pName].values) if self.logp
+                    y=-np.log10(highlight_tmp[self.pName].values)
+                    if self.logp
                     else highlight_tmp[self.pName].values,
                     mode="markers",
                     text=highlight_hover_text,
@@ -630,7 +603,7 @@ class _ManhattanPlot():
                         color=highlight_color,
                         size=point_size * 2,
                     ),
-                    name="SNP-Gene Pairs of interest"
+                    name="SNP-Gene Pairs of interest",
                 )
             )