Пример #1
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def plot_peaks(ax: Axes, peak_list: List[Peak.Peak], label: str = "Peaks", style: str = 'o') -> List[Line2D]:
	"""
	Plots the locations of peaks as found by PyMassSpec.

	:param ax: The axes to plot the peaks on
	:param peak_list: List of peaks to plot
	:param label: label for plot legend.
	:param style: The marker style. See `https://matplotlib.org/3.1.1/api/markers_api.html` for a complete list

	:return: A list of Line2D objects representing the plotted data.
	"""

	if not is_peak_list(peak_list):
		raise TypeError("'peak_list' must be a list of Peak objects")

	time_list = []
	height_list = []

	if "line" in style.lower():
		lines = []
		for peak in peak_list:
			lines.append(ax.axvline(x=peak.rt, color="lightgrey", alpha=0.8, linewidth=0.3))

		return lines

	else:
		for peak in peak_list:
			time_list.append(peak.rt)
			height_list.append(sum(peak.mass_spectrum.intensity_list))
			# height_list.append(peak.height)
			# print(peak.height - sum(peak.mass_spectrum.intensity_list))
			# print(sum(peak.mass_spectrum.intensity_list))

		return ax.plot(time_list, height_list, style, label=label)
Пример #2
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def store_peaks(peak_list: Peak,
                file_name: Union[str, pathlib.Path],
                protocol=1):
    """
        Store the list of peak objects

    :param peak_list: A list of peak objects
    :type peak_list: list of :class:`pyms.Peaks.Class.Peak`
    :param file_name: File name to store peak list
    :type file_name: str or os.PathLike
    :param protocol:
    :type protocol:

    :author: Andrew Isaac
    :author: Dominic Davis-Foster (type assertions and pathlib support)

    """

    if not is_peak_list(peak_list):
        raise TypeError("'peak_list' must be a list of Peak objects")

    if not is_path(file_name):
        raise TypeError("'file_name' must be a string or a PathLike object")

    file_name = prepare_filepath(file_name)

    fp = file_name.open('wb')
    pickle.dump(peak_list, fp, protocol)
    fp.close()
Пример #3
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    def __init__(self, expr_code: str, peak_list: Sequence[Peak]):
        if not isinstance(expr_code, str):
            raise TypeError("'expr_code' must be a string")

        if not is_peak_list(peak_list):
            raise TypeError("'peak_list' must be a list of Peak objects")

        self._expr_code = expr_code
        self._peak_list = list(peak_list)
Пример #4
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    def __init__(self, expr_code, peak_list):
        """
		Models an experiment
		"""

        if not isinstance(expr_code, str):
            raise TypeError("'expr_code' must be a string")
        if not is_peak_list(peak_list):
            raise TypeError("'peak_list' must be a list of Peak objects")

        self._expr_code = expr_code
        self._peak_list = peak_list
Пример #5
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def rel_threshold(pl: Sequence[Peak],
                  percent: float = 2,
                  copy_peaks: bool = True) -> List[Peak]:
    """
	Remove ions with relative intensities less than the given relative
	percentage of the maximum intensity.

	:param pl:
	:param percent: Threshold for relative percentage of intensity.
	:default percent: ``2%``
	:param copy_peaks: Whether the returned peak list should contain copies of the peaks.

	:return: A new list of Peak objects with threshold ions.

	:author: Andrew Isaac, Dominic Davis-Foster (type assertions)
	"""  # noqa: D400

    peak_list = pl

    if not is_peak_list(peak_list):
        raise TypeError("'pl' must be a list of Peak objects")
    if not is_number(percent):
        raise TypeError("'percent' must be a number > 0")

    if percent <= 0:
        raise ValueError("'percent' must be a number > 0")

    if copy_peaks:
        peak_list = copy.deepcopy(peak_list)

    new_peak_list = []
    for peak in peak_list:
        ms = peak.mass_spectrum
        # if ms is None:
        # 	raise ValueError("The peak has no mass spectrum.")

        ia = ms.mass_spec
        # assume max(ia) big so /100 1st
        cutoff = (max(ia) / 100.0) * float(percent)
        for i in range(len(ia)):
            if ia[i] < cutoff:
                ia[i] = 0
        ms.mass_spec = ia
        peak.mass_spectrum = ms
        new_peak_list.append(peak)

    return new_peak_list
Пример #6
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def num_ions_threshold(pl: List,
                       n: int,
                       cutoff: float,
                       copy_peaks: bool = True) -> List:
    """
    Remove Peaks where there are less than a given number of ion intensities above the given threshold

    :param pl: A list of Peak objects
    :type pl: list
    :param n: Minimum number of ions that must have intensities above the cutoff
    :type n: int
    :param cutoff: The minimum intensity threshold
    :type cutoff: int or float
    :param copy_peaks: Whether a the returned peak list should contain copies of the peaks. Default ``False``
    :type copy_peaks: bool, optional

    :return: A new list of Peak objects
    :rtype: list

    :author: Andrew Isaac, Dominic Davis-Foster (type assertions)
    """

    if not is_peak_list(pl):
        raise TypeError("'pl' must be a list of Peak objects")

    if not isinstance(n, int):
        raise TypeError("'n' must be an integer")

    if not isinstance(cutoff, Number):
        raise TypeError("'cutoff' must be a Number")

    if copy_peaks:
        pl = copy.deepcopy(pl)

    new_pl = []
    for p in pl:
        ms = p.mass_spectrum
        ia = ms.mass_spec
        ions = 0
        for i in range(len(ia)):
            if ia[i] >= cutoff:
                ions += 1
        if ions >= n:
            new_pl.append(p)

    return new_pl
Пример #7
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def rel_threshold(pl: List,
                  percent: float = 2,
                  copy_peaks: bool = True) -> List:
    """
    Remove ions with relative intensities less than the given relative percentage of the maximum intensity.

    :param pl: A list of Peak objects
    :type pl: list
    :param percent: Threshold for relative percentage of intensity. Default ``2%``
    :type percent: float, optional
    :param copy_peaks: Whether a the returned peak list should contain copies of the peaks. Default ``False``
    :type copy_peaks: bool, optional

    :return: A new list of Peak objects with threshold ions
    :rtype: list

    :author: Andrew Isaac, Dominic Davis-Foster (type assertions)
    """

    if not is_peak_list(pl):
        raise TypeError("'pl' must be a list of Peak objects")
    if not isinstance(percent, (int, float)):
        raise TypeError("'percent' must be a number > 0")

    if percent <= 0:
        raise ValueError("'percent' must be a number > 0")

    if copy_peaks:
        pl = copy.deepcopy(pl)

    new_pl = []
    for p in pl:
        ms = p.mass_spectrum
        ia = ms.mass_spec
        # assume max(ia) big so /100 1st
        cutoff = (max(ia) / 100.0) * float(percent)
        for i in range(len(ia)):
            if ia[i] < cutoff:
                ia[i] = 0
        ms.mass_spec = ia
        p.mass_spectrum = ms
        new_pl.append(p)

    return new_pl
Пример #8
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def num_ions_threshold(
    pl: Sequence[Peak],
    n: int,
    cutoff: float,
    copy_peaks: bool = True,
) -> List[Peak]:
    """
	Remove Peaks where there are fewer than ``n`` ions with intensities above the given threshold.

	:param pl:
	:param n: Minimum number of ions that must have intensities above the cutoff.
	:param cutoff: The minimum intensity threshold.
	:param copy_peaks: Whether the returned peak list should contain copies of the peaks.

	:return: A new list of Peak objects.

	:author: Andrew Isaac, Dominic Davis-Foster (type assertions)
	"""

    if not is_peak_list(pl):
        raise TypeError("'pl' must be a list of Peak objects")

    if not isinstance(n, int):
        raise TypeError("'n' must be an integer")

    if not is_number(cutoff):
        raise TypeError("'cutoff' must be a number")

    if copy_peaks:
        pl = copy.deepcopy(pl)

    new_pl = []
    for p in pl:
        ms = p.mass_spectrum
        ia = ms.mass_spec
        ions = 0
        for i in range(len(ia)):
            if ia[i] >= cutoff:
                ions += 1
        if ions >= n:
            new_pl.append(p)

    return new_pl
Пример #9
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def plot_peaks(ax, peak_list, label="Peaks", style="o"):
    """
	Plots the locations of peaks as found by PyMassSpec.

	:param ax: The axes to plot the peaks on
	:type ax: matplotlib.axes.Axes
	:param peak_list: List of peaks to plot
	:type peak_list: :class:`list` of :class:`pyms.Peak.Class.Peak` objects
	:param label: label for plot legend. Default ``Peaks``
	:type label: str, optional
	:param style: The marker style. See `https://matplotlib.org/3.1.1/api/markers_api.html` for a complete list
	:type style: str

	:return: A list of Line2D objects representing the plotted data.
	:rtype: list of :class:`matplotlib.lines.Line2D`
	"""

    if not is_peak_list(peak_list):
        raise TypeError("'peak_list' must be a list of Peak objects")

    time_list = []
    height_list = []

    if "line" in style.lower():
        lines = []
        for peak in peak_list:
            lines.append(
                ax.axvline(x=peak.rt,
                           color="lightgrey",
                           alpha=0.8,
                           linewidth=0.3))

        return lines

    else:
        for peak in peak_list:
            time_list.append(peak.rt)
            height_list.append(sum(peak.get_mass_spectrum().intensity_list))
            # height_list.append(peak.height)
            # print(peak.height - sum(peak.get_mass_spectrum().intensity_list))
            # print(sum(peak.mass_spectrum.intensity_list))

        return ax.plot(time_list, height_list, style, label=label)