geneview 0.3.0__py3-none-any.whl

geneview/__init__.py

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+__version__ = "0.3.0"
+
+import matplotlib
+
+from .palette import *
+from .utils import load_dataset, get_dataset_names
+from .karyotype import karyoplot
+from .baseplot import venn, generate_petal_labels
+from .gwas import manhattanplot, qqplot, qqnorm
+from .popgene import admixtureplot
+
+
+matplotlib.rcParams['ps.fonttype']     = 42
+matplotlib.rcParams['pdf.fonttype']    = 42
+matplotlib.rcParams['font.sans-serif'] = ["Arial","Lucida Sans","DejaVu Sans","Lucida Grande","Verdana"]
+matplotlib.rcParams['font.family']     = 'sans-serif'

geneview/_fastqplot.py

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+"""
+Functions for visulization fastq data
+"""
+from __future__ import print_function, division
+import numpy as np
+import matplotlib.pyplot as plt
+
+from .utils import get_color_cycle
+from .io import Fastq, FastqReader
+
+def fqqualplot(fqdata, phred=64, ax=None, title=None, 
+               xlabel=None, ylabel=None, **kwargs):
+    """
+    Plotting fastq data quality distribution.
+
+    Parameters
+    ----------
+    fqdata : Array like. A list of Fastq type data, array or Series
+        The input fastq data for plot.
+
+    phred : int, or 64, optional
+        The phred value to convert the base quality from ASCII to int
+        For Illumina fastq: 64(default)
+        For Sanger data: 33
+
+    ax : matplotlib axis, optional
+        Axes to plot on, otherwise use current axis.
+
+    title : string, or None, optional
+        If not None, set title on the plot
+
+    xlabel, ylabel : string,or None, optional
+        Set the x/y axis label of the current axis.
+
+    kwargs : key, values pairings, or None, optional
+        Other keyword arguments are passed to boxplot in
+        maplotlib.axis.Axes.boxplot.
+
+
+    Returns
+    -------
+    ax : matplotlib Axes
+        Axes object with the plot
+
+    Examples
+    --------
+
+    """
+    if ax is None:
+        ax = plt.gca()
+
+    if len(fqdata) == 0:
+        return ax
+
+    if 'showfliers' not in kwargs:
+        kwargs.setdefault("showfliers", False)
+
+    data = []
+    for r in fqdata:
+        # Convert base quality from ASCII to be integer
+        data.append([ord(b) - phred for b in r.qual])
+    data = np.array(data)
+
+    ax.boxplot(data, **kwargs)
+
+    # Set xtick
+    xticks = [i for i in range(0, len(data[0])+1, 10)]
+    ax.set_xticks(xticks)
+    ax.set_xticklabels(xticks)
+
+    ax.set_ylim(ymax=data.max()+1)
+    if title:
+        ax.set_title(title)
+    if xlabel:
+        ax.set_xlabel(xlabel)
+    if ylabel:
+        ax.set_ylabel(ylabel)
+
+    return ax
+
+
+def fastqreport(fqfile, fqfilelist=None):
+    """
+    Create a report for fastq data by input one fastq file or 
+    a fq file list.
+
+    Parameters
+    ----------
+
+    Returns
+    -------
+
+    Examples
+    --------
+
+    """
+    pass

geneview/_manhattan.py

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+"""Plotting functions for manhattan plot.
+
+Copyright (c) Shujia Huang
+Date: 2021-02-21
+
+This model is based on brentp's script on github:
+https://github.com/brentp/bio-playground/blob/master/plots/manhattan-plot.py
+
+Thanks for Brentp's contributions
+
+"""
+from itertools import cycle
+from pandas import DataFrame
+import numpy as np
+
+from matplotlib.pyplot import subplots
+from .utils import adjust_text
+
+
+# learn something from "https://github.com/reneshbedre/bioinfokit/blob/38fb4966827337f00421119a69259b92bb67a7d0/bioinfokit/visuz.py"
+def manhattanplot(data, chrom="#CHROM", pos="POS", pv="P", snp="ID", logp=True, ax=None,
+                  marker=".", color="#3B5488,#53BBD5", alpha=0.8,
+                  title=None, xlabel="Chromosome", ylabel=r"$-log_{10}{(P)}$",
+                  xtick_label_set=None, CHR=None, xticklabel_kws=None,
+                  suggestiveline=1e-5, genomewideline=5e-8, sign_line_cols="#D62728,#2CA02C", hline_kws=None,
+                  sign_marker_p=None, sign_marker_color="r",
+                  is_annotate_topsnp=False, text_kws=None, ld_block_size=50000, **kwargs):
+    """Creates a manhattan plot from PLINK assoc output (or any data frame with chromosome, position, and p-value).
+
+    Parameters
+    ----------
+    data : DataFrame.
+        A DataFrame with columns "#CHROM," "POS," "P," and optionally, "SNP."
+
+    chrom : string, default is "#CHROM", optional
+        A string denoting the column name for chromosome. Defaults to be PLINK2.x's "#CHROM".
+        Said column must be a character.
+
+    pos : string, default is "POS", optional.
+        A string denoting the column name for chromosomal position. Default to PLINK2.x's "POS".
+        Said column must be numeric.
+
+    pv : string, default is "P", optional.
+        A string denoting the column name for chromosomal p-value. Default to PLINK2.x's "P".
+        Said column must be float type.
+
+    snp : string, default is "ID", optional.
+        A string denoting the column name for the SNP name (rs number) or the column which you want to
+        represent the variants. Default to PLINK2.x's "P". Said column should be a character.
+
+    logp : bool, optional
+        If TRUE, the -log10 of the p-value is plotted. It isn't very useful
+        to plot raw p-values, but plotting the raw value could be useful for
+        other genome-wide plots, for example, peak heights, bayes factors, test
+        statistics, other "scores," etc. default: True
+
+    ax : matplotlib axis, optional
+        Axis to plot on, otherwise uses current axis.
+
+    marker : matplotlib markers for scatter plot, default is "o", optional
+
+    color : matplotlib color, optional, defauft: "#3B5488,#53BBD5"
+        Color used for the plot elements. Could hex-code or rgb,
+        e.g: '#3B5488,#53BBD5' or 'rb'
+
+    alpha : float scalar, default is 0.8, optional
+        The alpha blending value, between 0(transparent) and 1(opaque)
+
+    title : string, or None, optional
+        Set the title of the current plot.
+
+    xlabel: string, optional
+        Set the x axis label of the current axis.
+
+    ylabel: string, optional
+        Set the y axis label of the current axis.
+
+    xtick_label_set : a set. optional
+        Set the current x axis ticks of the current axis.
+
+    CHR : string, or None, optional
+        Select a specific chromosome to plot. And the x-axis will be the
+        position of this chromosome instead of the chromosome id.
+
+        CAUTION: this parameter could not be used with ``xtick_label_set``
+                 together.
+
+    xticklabel_kws : key, value pairings, or None, optional
+        Other keyword arguments are passed to set xtick labels in
+        maplotlib.axis.Axes.set_xticklabels.
+
+    suggestiveline : float or None, default is 1e-5, optional
+        Where to draw a suggestive ax.axhline. Set None to be disable.
+
+    genomewideline : float or None, default is 5e-8
+        Where to draw a genome-wide significant ax.axhline. Set None to be disable.
+
+    sign_line_cols : matplotlib color, default: "#D62728,#2CA02C", optional.
+        Color used for ``suggestiveline`` and ``genomewideline``.
+        Could be hex-code or rgb, e.g: "#D62728,#2CA02C" or 'rb'
+
+    hline_kws : key, value pairings, or None, optional
+        keyword arguments for plotting ax.axhline(``suggestiveline`` and ``genomewideline``)
+        except the "color" key-pair.
+
+    sign_marker_p : float or None, default None, optional.
+        A P-value threshold (suggestive to be 1e-6) for marking the significant SNP sites.
+
+    sign_marker_color : matplotlib color, default: "r", optional.
+        Define a color code for significant SNP sites.
+
+    is_annotate_topsnp : boolean, default is False, optional.
+        Annotate the top SNP or not for the significant locus.
+
+    text_kws: key, value pairings, or None, optional
+        keyword arguments for plotting plt.annotate in`` matplotlib.axes.Axes.text(x, y, s, fontdict=None, **kwargs)``
+
+    ld_block_size : integer, default is 50000, optional
+        Set the size of LD block which for finding top SNP. And the top SNP's annotation represent the block.
+
+    kwargs : key, value pairings, optional
+        Other keyword arguments are passed to ``plt.scatter()`` or
+        ``plt.vlines()`` (in matplotlib.pyplot) depending on whether 
+        a scatter or line plot is being drawn.
+
+
+    Returns
+    -------
+    ax : matplotlib Axes
+        Axes object with the manhattanplot.
+
+    Notes
+    -----
+    1. This plot function is not just suit for GWAS manhattan plot,
+       it could also be used for any input data which have [chromo-
+       some, position and p-value] dataframe.
+
+    2. The right and top spines of the plot have been set to be
+       invisible by hand.
+
+    Examples
+    --------
+
+    Plot a basic manhattan plot from PLINK2.x association output and reture the figure:
+
+    .. plot::
+        :context: close-figs
+
+        >>> import pandas as pd
+        >>> from geneview import manhattanplot
+        >>> from geneview.utils import load_dataset
+        >>> df = load_dataset("gwas")
+        >>> ax = manhattanplot(data=df)
+
+    Plot a basic manhattan plot with horizontal xtick labels:
+
+    .. plot::
+        :context: close-figs
+
+        >>> xtick = set(['chr' + i for i in list(map(str, range(1, 10))) + ['11', '13', '15', '18', '21', 'X']])
+        >>> manhattanplot(data=df, xlabel="Chromosome", ylabel=r"$-log_{10}{(P)}$",
+        ...               xtick_label_set=xtick)
+
+    Add a horizontal at y position=3 line with linestyle="--" and lingwidth=1.3
+    across the axis:
+
+    .. plot::
+        :context: close-figs
+    
+        >>> manhattanplot(data=df,
+        ...               hline_kws={"linestyle": "--", "lw": 1.3},
+        ...               xlabel="Chromosome",
+        ...               ylabel=r"$-log_{10}{(P)}$",
+        ...               xtick_label_set = xtick)
+
+    Rotate the x-axis ticklabel by setting ``xticklabel_kws``:
+
+    .. plot::
+        :context: close-figs
+
+        >>> manhattanplot(data=df,
+        ...               hline_kws={"linestyle": "--", "lw": 1.3},
+        ...               xlabel="Chromosome",
+        ...               ylabel=r"$-log_{10}{(P)}$",
+        ...               xticklabel_kws={"rotation": "vertical"})
+
+    Plot a better one with genome-wide significant mark and annotate the Top SNP and save
+    the figure to "output_manhattan_plot.png":
+
+    .. plot::
+        :context: close-figs
+
+        >>> fig, ax = plt.subplots(figsize=(12, 4), facecolor="w", edgecolor="k")  # define a plot
+        >>> manhattanplot(data=df,
+        ...               marker=".",
+        ...               sign_marker_p=1e-6,  # Genome wide significant p-value
+        ...               sign_marker_color="r",
+        ...               snp="ID",
+        ...               title="Test",
+        ...               xtick_label_set=xtick,
+        ...               xlabel="Chromosome",
+        ...               ylabel=r"$-log_{10}{(P)}$",
+        ...               sign_line_cols=["#D62728", "#2CA02C"],
+        ...               hline_kws={"linestyle": "--", "lw": 1.3},
+        ...               is_annotate_topsnp=True,
+        ...               ld_block_size=50000,  # 50000 bp
+        ...               annotext_kws={"fontsize": 12,  # The fontsize of annotate text
+        ...                             "arrowprops": dict(arrowstyle="-", color="k", alpha=0.6)},
+        ...               ax=ax)
+    """
+    if not isinstance(data, DataFrame):
+        raise ValueError("[ERROR] Input data must be a pandas.DataFrame.")
+    if chrom not in data:
+        raise ValueError("[ERROR] Column \"%s\" not found!" % chrom)
+    if pos not in data:
+        raise ValueError("[ERROR] Column \"%s\" not found!" % pos)
+    if pv not in data:
+        raise ValueError("[ERROR] Column \"%s\" not found!" % pv)
+    if is_annotate_topsnp and (snp not in data):
+        raise ValueError("[ERROR] You're trying to annotate a set of SNPs but "
+                         "NO SNP \"%s\" column found!" % snp)
+    if CHR is not None and xtick_label_set is not None:
+        raise ValueError("[ERROR] ``CHR`` and ``xtick_label_set`` can't be set simultaneously.")
+
+    data[[chrom]] = data[[chrom]].astype(str)  # make sure all the chromosome id are character.
+
+    # Draw the plot and return the Axes
+    if ax is None:
+        # ax = plt.gca()
+        _, ax = subplots(figsize=(9, 3), facecolor="w", edgecolor="k")  # default
+
+    if xticklabel_kws is None:
+        xticklabel_kws = {}
+    if hline_kws is None:
+        hline_kws = {}
+    if text_kws is None:
+        text_kws = {}
+
+    if "," in color:
+        color = color.split(",")
+    colors = cycle(color)
+
+    last_xpos = 0
+    xs_by_id = []  # use for collecting chromosome's position on x-axis
+    x, y, c = [], [], []
+    sign_snp_sites = []
+    for seqid, group_data in data.groupby(by=chrom, sort=False):  # keep the raw order of chromosome
+
+        if (CHR is not None) and (seqid != CHR):
+            continue
+
+        color = next(colors)
+        for i, (site, p_value) in enumerate(zip(group_data[pos], group_data[pv])):
+            y_value = -np.log10(p_value) if logp else p_value
+
+            x.append(last_xpos + site)
+            y.append(y_value)
+
+            c.append(sign_marker_color if ((sign_marker_p is not None) and (p_value <= sign_marker_p)) else color)
+            if (sign_marker_p is not None) and (p_value <= sign_marker_p):
+                snp_id = group_data[snp].iloc[i]
+                sign_snp_sites.append([last_xpos + site, y_value, snp_id])  # x_pos, y_value, text
+
+        # ``xs_by_id`` is for setting up positions and ticks. Ticks should
+        # be placed in the middle of a chromosome. The a new pos column is 
+        # added that keeps a running sum of the positions of each successive 
+        # chromsome.
+        xs_by_id.append([seqid, last_xpos + (group_data[pos].iloc[0] + group_data[pos].iloc[-1]) / 2])
+        last_xpos = x[-1]  # keep track so that chromosome will not overlap in the plot.
+
+    if not x:
+        raise ValueError("zero-size array to reduction operation minimum which has no "
+                         "identity. This could be caused by zero-size array of ``x`` "
+                         "in the ``manhattanplot(...)`` function.")
+
+    if "marker" not in kwargs:
+        kwargs["marker"] = marker
+
+    # plot the main manhattan dot plot
+    ax.scatter(x, y, c=c, alpha=alpha, edgecolors="none", **kwargs)
+
+    if is_annotate_topsnp is not None:
+        index = _find_SNPs_which_overlap_sign_neighbour_region(
+            sign_snp_neighbour_region=_sign_snp_regions(sign_snp_sites, ld_block_size),
+            x=x)
+
+        # reset color for all SNPs which nearby the top SNPs.
+        for i in index:
+            ax.scatter(x[i], y[i], c=sign_marker_color, alpha=alpha, edgecolors="none", **kwargs)
+
+    # Add GWAS significant lines
+    if "color" in hline_kws:
+        hline_kws.pop("color")
+
+    sign_line_cols = sign_line_cols.split(",") if "," in sign_line_cols else sign_line_cols
+    if suggestiveline is not None:
+        ax.axhline(y=-np.log10(suggestiveline) if logp else suggestiveline, color=sign_line_cols[0], **hline_kws)
+    if genomewideline is not None:
+        ax.axhline(y=-np.log10(genomewideline) if logp else genomewideline, color=sign_line_cols[1], **hline_kws)
+
+    # Plotting the Top SNP for each significant block
+    if is_annotate_topsnp:
+        sign_top_snp = _find_top_snp(sign_snp_sites, ld_block_size=ld_block_size, is_get_biggest=logp)
+        if sign_top_snp:  # not empty
+            texts = [ax.text(_x, _y, _text) for _x, _y, _text in sign_top_snp]
+            adjust_text(texts, ax=ax, **text_kws)
+
+    if CHR is None:
+
+        if xtick_label_set is not None:
+            ax.set_xticks([v for c, v in xs_by_id if c in xtick_label_set])
+            ax.set_xticklabels([c for c, v in xs_by_id if c in xtick_label_set], **xticklabel_kws)
+        else:
+            ax.set_xticks([v for c, v in xs_by_id])
+            ax.set_xticklabels([c for c, v in xs_by_id], **xticklabel_kws)
+
+    else:
+        # show the whole chromosomal position without scientific notation
+        # if you are just interesting in this chromosome.
+        ax.get_xaxis().get_major_formatter().set_scientific(False)
+
+    ax.set_xlim(0, x[-1])
+    ax.set_ylim(ymin=min(y), ymax=1.2 * max(y))
+
+    if title:
+        ax.set_title(title)
+    if xlabel:
+        ax.set_xlabel(xlabel)
+    if ylabel:
+        ax.set_ylabel(ylabel)
+
+    ax.spines["top"].set_visible(False)
+    ax.spines["right"].set_visible(False)
+    return ax
+
+
+def _find_top_snp(sign_snp_data, ld_block_size, is_get_biggest=True):
+    """
+    :param sign_snp_data:  A 2D array: [[xpos1, yvalue1, text1], [xpos2, yvalue2, text2], ...]
+    """
+    top_snp = []
+    tmp_cube = []
+    for i, (_x, _y, text) in enumerate(sign_snp_data):
+        if i == 0:
+            tmp_cube.append([_x, _y, text])
+            continue
+
+        if _x > tmp_cube[-1][0] + ld_block_size:
+            # Sorted by y_value in increase/decrease order and only get the first value [0], which is the TopSNP.
+            top_snp.append(sorted(tmp_cube, key=(lambda x: x[1]), reverse=is_get_biggest)[0])
+            tmp_cube = []
+
+        tmp_cube.append([_x, _y, text])
+
+    if tmp_cube:  # deal the last one
+        top_snp.append(sorted(tmp_cube, key=(lambda x: x[1]), reverse=True)[0])
+
+    return top_snp
+
+
+def _sign_snp_regions(sign_snp_data, ld_block_size):
+    """Create region according to the coordinate of sign_snp_data."""
+    regions = []
+    for i, (_x, _y, _t) in enumerate(sign_snp_data):
+        if i == 0:
+            regions.append([_x - ld_block_size, _x])
+            continue
+
+        if _x > regions[-1][1] + ld_block_size:
+            regions[-1][1] += ld_block_size
+            regions.append([_x - ld_block_size, _x])
+        else:
+            regions[-1][1] = _x
+
+    # The last
+    if regions:
+        regions[-1][1] += ld_block_size
+
+    return regions
+
+
+def _find_SNPs_which_overlap_sign_neighbour_region(sign_snp_neighbour_region, x):
+    """
+    """
+    x_size = len(x)
+    reg_size = len(sign_snp_neighbour_region)
+    index = []
+    tmp_index = 0
+    for i in range(x_size):
+        _x = x[i]
+
+        is_overlap = False
+        iter_index = range(tmp_index, reg_size)
+        for j in iter_index:
+            if _x > sign_snp_neighbour_region[j][1]: continue
+            if _x < sign_snp_neighbour_region[j][0]: break
+
+            tmp_index = j
+            is_overlap = True
+            break
+
+        if is_overlap:
+            index.append(i)
+
+    # return the index
+    return index