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correlation_window.py
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from os import path
from PyQt5 import QtCore, QtWidgets
from PyQt5.uic import loadUi
from utilities import *
class CorrelationDialog(QtWidgets.QDialog):
def __init__(self, main_dialog, parent=None):
super(CorrelationDialog, self).__init__(parent)
self.setWindowFlags(self.windowFlags() & QtCore.Qt.WindowMinimizeButtonHint)
# populate the Window from our *.ui file which was created with the Qt Designer
uifile = path.join(path.dirname(__file__), 'GUIs/correlated.ui')
loadUi(uifile, self)
self.parent = main_dialog
self.current_obj = None
self.show_corr.clicked.connect(self.show_corr_fn)
self.text_filter.textChanged.connect(self.filter_table)
def create_table(self, obj):
try:
import numpy as np
import pandas as pd
except ImportError:
self.parent.log("Please install numpy and pandas to use this plugin")
return
df = pd.DataFrame()
freq_inter = get_freq(obj, self.parent.temp_dir.name)
freq_combined = get_freq_combined_all_interactions(obj, self.parent.temp_dir.name)
self.current_obj = obj
tableWidget = self.corrTable
for inter in list(intTypeMap.keys()) + ["ALL"]:
edges, corr_matr, p_matr = self.parent.correlations[obj][inter]
with np.errstate(divide='ignore', invalid='ignore'):
indexes = np.argwhere(~np.isnan(corr_matr))
edge1s = [edges[x] for x in [y[0] for y in indexes]]
freqs1 = [freq_inter[inter][edge] if inter != 'ALL' else freq_combined[edge] for edge in edge1s]
inter_labels = [inter for _ in edge1s]
edge2s = [edges[x] for x in [y[1] for y in indexes]]
freqs2 = [freq_inter[inter][edge] if inter != 'ALL' else freq_combined[edge] for edge in edge2s]
corr_vals = [corr_matr[i, j] for (i, j) in indexes]
p_vals = [p_matr[i, j] for (i, j) in indexes]
tableWidget.setRowCount(0)
tableWidget.setSortingEnabled(False)
rowPosition = tableWidget.rowCount() # necessary even when there are no rows in the table
df_of_interaction = pd.DataFrame(
[edge1s, freqs1, inter_labels, edge2s, freqs2, corr_vals, p_vals]).transpose()
df = pd.concat([df, df_of_interaction])
self.parent.log("{} {} interactions correlates/anti-correlates".format(len(df_of_interaction), inter))
df = df.sort_values([0, 3, 5], ascending=(True, True, False))
prev_edge = None
color = 2
tableWidget.horizontalHeader().setSectionResizeMode(QtWidgets.QHeaderView.Stretch)
for _, row in df.iterrows():
x, f1, p, y, f2, z, w, *_ = row.to_list()
if x != prev_edge:
bg_color, fg_color, color = get_bg_fg_colors(color)
tableWidget.insertRow(rowPosition)
tableWidget.setItem(rowPosition, 0, QtWidgets.QTableWidgetItem(str(x)))
f1Item = QtWidgets.QTableWidgetItem()
f1Item.setData(QtCore.Qt.EditRole, round(float(f1), 3))
tableWidget.setItem(rowPosition, 1, f1Item)
tableWidget.setItem(rowPosition, 2, QtWidgets.QTableWidgetItem(p))
tableWidget.setItem(rowPosition, 3, QtWidgets.QTableWidgetItem(str(y)))
f2Item = QtWidgets.QTableWidgetItem()
f2Item.setData(QtCore.Qt.EditRole, round(float(f2), 3))
tableWidget.setItem(rowPosition, 4, f2Item)
zItem = QtWidgets.QTableWidgetItem()
zItem.setData(QtCore.Qt.EditRole, round(float(z), 2))
tableWidget.setItem(rowPosition, 5, zItem)
wItem = QtWidgets.QTableWidgetItem()
wItem.setData(QtCore.Qt.EditRole, float(w))
tableWidget.setItem(rowPosition, 6, wItem)
for i in range(7):
tableWidget.item(rowPosition, i).setBackground(bg_color)
tableWidget.item(rowPosition, i).setForeground(fg_color)
tableWidget.item(rowPosition, i).setTextAlignment(QtCore.Qt.AlignCenter)
if z > 0:
tableWidget.item(rowPosition, 5).setForeground(QColor(0, 0, 255))
else:
tableWidget.item(rowPosition, 5).setForeground(QColor(255, 0, 0))
prev_edge = x
rowPosition += 1
tableWidget.setSortingEnabled(True)
tableWidget.viewport().update()
self.show()
def filter_table(self):
filters = self.text_filter.toPlainText().strip().split(' ')
tableWidget = self.corrTable
if len(filters) > 0:
to_filter_total = set()
for f in filters:
to_filter = set()
items = tableWidget.findItems(f, QtCore.Qt.MatchContains)
for item in items:
to_filter.add(item.row())
if len(to_filter_total) == 0:
to_filter_total = to_filter
else:
to_filter_total.intersection_update(to_filter)
for row in range(tableWidget.rowCount()):
tableWidget.setRowHidden(row, row not in to_filter_total)
def show_corr_fn(self):
self.parent.disable_window()
cmd.delete("edge1 edge2 edge1_cgo edge2_cgo")
table = self.corrTable
selection = table.selectionModel().selectedRows()
if len(selection) == 0:
self.parent.log("Please select at least one row first!", error=True)
return
for i in range(len(selection)):
row = selection[i].row()
edge1 = table.item(row, 0).text()
edge2 = table.item(row, 3).text()
edge1 = Edge([Node(node) for node in edge1.split(' - ')])
edge2 = Edge([Node(node) for node in edge2.split(' - ')])
print(edge1, edge2)
cmd.select("edge1", "/{}//{}/{} or /{}//{}/{}".format(self.current_obj, edge1.node1.chain, edge1.node1.resi,
self.current_obj, edge1.node2.chain,
edge1.node2.resi), merge=1)
cmd.select("edge2", "/{}//{}/{} or /{}//{}/{}".format(self.current_obj, edge2.node1.chain, edge2.node1.resi,
self.current_obj, edge2.node2.chain,
edge2.node2.resi), merge=1)
inter = 'ALL' if len(selection) > 1 else table.item(selection[0].row(), 2).text()
self.parent.visualize(selection="edge1", of_type=inter)
self.parent.visualize(selection="edge2", of_type=inter)
self.parent.log("Selection edge1 contains all the residues from the edges selected in the first column",
timed=False)
self.parent.log("Selection edge2 contains all the residues from the edges selected in the second column",
timed=False)
self.parent.log(
"CGO objects edge1_cgo and edge2_cgo are the selected edges from the first and second column respectively",
timed=False)
self.parent.enable_window()