Merge pull request #2 from choderalab/plate_reader

Plate_reader

fluorescence_assay/plate_reader.py

@@ -1 +1,80 @@
-"""Comment."""
+"""Module to parse plate reader outputs."""
+
+import logging
+from abc import ABC, abstractmethod
+from dataclasses import dataclass, field
+from typing import Optional
+
+from bs4 import BeautifulSoup
+
+logger = logging.getLogger(__name__)
+
+
+@dataclass
+class Measurements(ABC):
+    """"""
+
+    @abstractmethod
+    def read_file(self, filepath: str, *args, **kwargs) -> None:
+        """"""
+        ...
+
+    @abstractmethod
+    def get_well(self, *args, **kwargs) -> dict:
+        """"""
+        ...
+
+    @abstractmethod
+    def get_parameter(self, *args, **kwargs):
+        """"""
+        ...
+
+
+@dataclass
+class IControlXML(Measurements):
+    """"""
+
+    _data: dict = field(default_factory=dict, init=False)
+
+    def read_file(self, filepath: str, filter: Optional[list[str]] = None) -> None:
+        """"""
+
+        with open(filepath) as file:
+            self._data = BeautifulSoup(file, "xml")
+
+    def get_data(self):
+        """"""
+
+        return self._data
+
+    def get_well(self, section, well, cycle: Optional[int] = 1):
+        """"""
+
+        def fix_type(val):
+            try:
+                return float(val)
+            except:
+                return float("nan")
+
+        data = {
+            int(scan["WL"]): fix_type(scan.contents[0])
+            for scan in self._data.select(
+                f'Section[Name="{section}"] > Data[Cycle="{str(cycle)}"] > Well[Pos="{well}"] > Scan'
+            )
+        }
+
+        return data
+
+    def get_parameter(self, section, parameter):
+
+        def fix_type(val):
+            try:
+                return float(val)
+            except:
+                return val
+
+        return fix_type(
+            self._data.select(
+                f'Section[Name="{section}"] > Parameters > Parameter[Name="{parameter}"]'
+            )[0]["Value"]
+        )

fluorescence_assay/plotting.py

@@ -0,0 +1,191 @@
+"""Module to plot parsed plate reader ouptputs."""
+
+from abc import ABC, abstractmethod
+from dataclasses import dataclass, field
+from typing import Optional
+
+import matplotlib
+import matplotlib.axes
+import matplotlib.pyplot as plt
+import numpy as np
+
+from .plate_reader import IControlXML, Measurements
+
+
+@dataclass
+class Plot(ABC):
+    """"""
+
+    @abstractmethod
+    def load_data(self, Measurement: Measurements, *args, **kwargs) -> None:
+        """"""
+        ...
+
+    def format_plot(
+        self,
+        axes: matplotlib.axes._axes.Axes,
+        title: Optional[str] = None,
+        xlim: Optional[list[float]] = None,
+        ylim: Optional[list[float]] = None,
+        xlabel: Optional[str] = None,
+        ylabel: Optional[str] = None,
+        square: Optional[bool] = False,
+    ):
+
+        if title is not None:
+            axes.set_title(title)
+
+        if xlim is not None:
+            axes.set_xlim(xlim)
+
+        if ylim is not None:
+            axes.set_ylim(ylim)
+
+        if xlabel is not None:
+            axes.set_xlabel(xlabel)
+
+        if ylabel is not None:
+            axes.set_ylabel(ylabel)
+
+        if square == True:
+            axes.set_box_aspect(1)
+
+
+@dataclass
+class IControlXMLPlot(Plot):
+    """"""
+
+    _plate_read: dict = field(default_factory=dict, init=False)
+
+    def load_data(self, IControlXML: IControlXML) -> None:
+
+        self._plate_read = IControlXML
+
+    def get_wavelength_axis(self, section) -> np.ndarray:
+
+        lmin, lmax, lstep = (
+            self._plate_read.get_parameter(section, parameter)
+            for parameter in [
+                "Emission Wavelength Start",
+                "Emission Wavelength End",
+                "Emission Wavelength Step Size",
+            ]
+        )
+
+        return np.arange(lmin, lmax + lstep, lstep)
+
+    def plot_well_spectrum(
+        self,
+        axes: matplotlib.axes._axes.Axes,
+        section: str,
+        well: str,
+        cycle: Optional[int] = 1,
+        color: Optional[tuple] = (0, 0, 0),
+        label: Optional[str] = None,
+    ) -> None:
+
+        data = np.array(list(self._plate_read.get_well(section, well, cycle).values()))
+
+        ll = self.get_wavelength_axis(section)
+
+        axes.plot(ll, data, color=color, label=label)
+
+    def plot_corrected_spectrum(
+        self,
+        axes: matplotlib.axes._axes.Axes,
+        section: str,
+        well_foreground: str,
+        well_background: str,
+        cycle: Optional[int] = 1,
+        color: Optional[tuple] = (0, 0, 0),
+        label: Optional[str] = None,
+    ) -> None:
+
+        foreground = np.array(
+            list(self._plate_read.get_well(section, well_foreground, cycle).values())
+        )
+        background = np.array(
+            list(self._plate_read.get_well(section, well_background, cycle).values())
+        )
+
+        difference = foreground - background
+
+        ll = self.get_wavelength_axis(section)
+
+        axes.plot(ll, difference, color=color, label=label)
+
+    def plot_dose_response(
+        self,
+        axes: matplotlib.axes._axes.Axes,
+        section: str,
+        row_foreground: str,
+        row_background: str,
+        wavelength: int,
+        concentrations: list[float],
+        cycle: Optional[int] = 1,
+        color: Optional[tuple] = (0, 0, 0),
+        label: Optional[str] = None,
+    ) -> None:
+
+        differences = []
+
+        for i in range(len(concentrations)):
+
+            foreground = self._plate_read.get_well(
+                section, f"{row_foreground}{i+1}", cycle
+            )[wavelength]
+            background = self._plate_read.get_well(
+                section, f"{row_background}{i+1}", cycle
+            )[wavelength]
+
+            difference = foreground - background
+
+            differences.append(difference)
+
+        axes.plot(concentrations, differences, ".", color=color, label=label)
+
+    def plot_absorption_spectrum(
+        self,
+        axes: matplotlib.axes._axes.Axes,
+        section: str,
+        well: str,
+        cycle: Optional[int] = 1,
+        color: Optional[tuple] = (0, 0, 0),
+        label: Optional[str] = None,
+    ) -> None:
+
+        data = np.array(list(self._plate_read.get_well(section, well, cycle).values()))
+
+        lmin, lmax, lstep = (
+            # hardcoding these values temporarily
+            # TODO: Undo this!
+            240,
+            800,
+            5,
+        )
+
+        ll = np.arange(lmin, lmax + lstep, lstep)
+
+        axes.plot(ll, data, color=color, label=label)
+
+    def plot_absorption_across_row(
+        self,
+        axes: matplotlib.axes._axes.Axes,
+        section: str,
+        row: str,
+        wavelength: int,
+        concentrations: list[float],
+        cycle: Optional[int] = 1,
+        color: Optional[tuple] = (0, 0, 0),
+        label: Optional[str] = None,
+    ) -> None:
+
+        values = []
+
+        for i in range(len(concentrations)):
+
+            value = self._plate_read.get_well(section, f"{row}{i+1}", cycle)[wavelength]
+
+            values.append(value)
+
+        axes.plot(concentrations, values, ".", color=color, label=label)