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hcjihcji
committedDec 2, 2021
0.99.5b
·
version_0.99.5
1 parent 58b0d4d commit 7fbff37

14 files changed

+499
-293
lines changed
 

‎AnalTPP2D.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -211,7 +211,7 @@ def setupUi(self, Form):
211211
self.gridLayout.addWidget(self.splitter, 0, 0, 1, 1)
212212

213213
self.retranslateUi(Form)
214-
self.tabWidget.setCurrentIndex(0)
214+
self.tabWidget.setCurrentIndex(1)
215215
QtCore.QMetaObject.connectSlotsByName(Form)
216216

217217
def retranslateUi(self, Form):

‎AnalTPP2D.ui

+1-1
Original file line numberDiff line numberDiff line change
@@ -298,7 +298,7 @@
298298
</font>
299299
</property>
300300
<property name="currentIndex">
301-
<number>0</number>
301+
<number>1</number>
302302
</property>
303303
<widget class="QWidget" name="vocano">
304304
<property name="font">

‎AnalTPP2DUI.py

+2-2
Original file line numberDiff line numberDiff line change
@@ -28,10 +28,10 @@
2828
'''
2929

3030

31-
class AnalTPP2D(QtWidgets.QWidget, Ui_Form):
31+
class AnalTPP2DUI(QtWidgets.QWidget, Ui_Form):
3232

3333
def __init__(self, parent=None):
34-
super(AnalTPP2D, self).__init__(parent)
34+
super(AnalTPP2DUI, self).__init__(parent)
3535
self.setupUi(self)
3636
self.setWindowTitle("TPP2D Analysis")
3737
self.setWindowIcon(QtGui.QIcon("img/TPCA.ico"))

‎AnalTSAUI.py

+12-6
Original file line numberDiff line numberDiff line change
@@ -110,11 +110,14 @@ def __init__(self, parent=None):
110110
self.minR2_TPP = 0.8
111111
self.maxPlateau_TPP = 0.3
112112
self.repCheck_TPP = 'True'
113+
self.pthres1_TPP = 0.05
114+
self.pthres2_TPP = 0.1
115+
self.min_slope_TPP = -0.06
113116
self.minR2_NP_Null = 0.8
114117
self.minR2_NP_Alt = 0.8
115118
self.maxPlateau_NP = 0.3
116-
self.minR2_Infl = 0.8
117-
self.numSD_Infl = 2
119+
# self.minR2_Infl = 0.8
120+
# self.numSD_Infl = 2
118121
self.Metr_Dist = 'cityblock'
119122
self.minR2_Dist = 0.8
120123
self.maxPlateau_Dist = 0.3
@@ -147,11 +150,14 @@ def SetParams(self):
147150
self.minR2_TPP = self.ParamTSAUI.BoxR2.value()
148151
self.maxPlateau_TPP = self.ParamTSAUI.BoxPla.value()
149152
self.repCheck_TPP = self.ParamTSAUI.BoxCheck.currentText()
153+
self.pthres1_TPP = self.ParamTSAUI.BoxPval1.value()
154+
self.pthres2_TPP = self.ParamTSAUI.BoxPval2.value()
155+
self.min_slope_TPP = self.ParamTSAUI.BoxMinSlope.value()
150156
self.minR2_NP_Null = self.ParamTSAUI.BoxR2_Null.value()
151157
self.minR2_NP_Alt = self.ParamTSAUI.BoxR2_Alt.value()
152158
self.maxPlateau_NP = self.ParamTSAUI.BoxPlaN.value()
153-
self.minR2_Infl = self.ParamTSAUI.BoxR2_Infl.value()
154-
self.numSD_Infl = self.ParamTSAUI.BoxNumSD.value()
159+
# self.minR2_Infl = self.ParamTSAUI.BoxR2_Infl.value()
160+
# self.numSD_Infl = self.ParamTSAUI.BoxNumSD.value()
155161
self.Metr_Dist = self.ParamTSAUI.BoxMetrics.currentText()
156162
self.minR2_Dist = self.ParamTSAUI.BoxR2_Dist.value()
157163
self.maxPlateau_Dist = self.ParamTSAUI.BoxPla_Dist.value()
@@ -428,7 +434,7 @@ def VisualizeTPP(self):
428434
res = res[['Accession', 'Score', 'Rep1pVal (-log10)', 'Rep1delta_Tm', 'Rep1Group1_R2', 'Rep1Group2_R2', 'Rep1Group1_Tm', 'Rep1Group2_Tm', 'Rep1min_Slope',
429435
'Rep2pVal (-log10)', 'Rep2delta_Tm', 'Rep2Group1_R2', 'Rep2Group2_R2', 'Rep2Group1_Tm', 'Rep2Group2_Tm', 'Rep2min_Slope']]
430436
if self.repCheck_TPP == 'True':
431-
res = ReplicateCheck(res)
437+
res = ReplicateCheck(res, self.pthres1_TPP, self.pthres2_TPP, self.min_slope_TPP)
432438

433439
resultTable = res.sort_values(by = 'Score', axis = 0, ascending = False)
434440
self.resultData = []
@@ -596,7 +602,7 @@ def VisualizeDist(self):
596602
res = res[['Accession', 'Score', 'pVal (-log10)', 'Rep1delta_SH', 'Rep2delta_SH', 'Rep1Group1_R2', 'Rep1Group2_R2', 'Rep1Group1_SH', 'Rep1Group2_SH', 'Rep1min_Slope',
597603
'Rep2Group1_R2', 'Rep2Group2_R2', 'Rep2Group1_SH', 'Rep2Group2_SH', 'Rep2min_Slope']]
598604
if self.repCheck_TPP == 'True':
599-
res = ReplicateCheck(res)
605+
res = ReplicateCheck(res, self.pthres1_TPP, self.pthres2_TPP, self.min_slope_TPP)
600606
resultTable = res.sort_values(by = 'Score', axis = 0, ascending = False)
601607
self.resultData = []
602608
self.resultTable = resultTable

‎MakeFigure.py

+33-31
Original file line numberDiff line numberDiff line change
@@ -63,9 +63,10 @@ def ProteinComplexFigure(self, proteinSubunit, proteinData, colNames):
6363
self.axes.scatter(temps, vec, marker='.', label = p, s = 15)
6464
self.axes.plot(temps_, meltCurve(temps_, paras[0], paras[1], paras[2]), lw = 1)
6565

66-
self.axes.set_xlabel('Temperature (℃)', fontsize=5)
67-
self.axes.set_ylabel('Abundances', fontsize=5)
68-
self.axes.legend(fontsize=4, bbox_to_anchor=(1,1), loc="upper left")
66+
self.axes.set_xlabel('Temperature (℃)', fontsize=6)
67+
self.axes.set_ylabel('Abundances', fontsize=6)
68+
self.axes.tick_params(labelsize=5)
69+
self.axes.legend(fontsize=4.5, bbox_to_anchor=(1,1), loc="upper left")
6970
self.draw()
7071

7172

@@ -83,9 +84,9 @@ def AverageTSAFigure(self, proteinData1, proteinData2, colNames):
8384
self.axes.plot(temps, vec_2, label = 'Group 2')
8485

8586
self.axes.tick_params(labelsize=4)
86-
self.axes.set_xlabel('Temperature (℃)', fontsize=3)
87-
self.axes.set_ylabel('Abundances', fontsize=3)
88-
self.axes.legend(fontsize=3)
87+
self.axes.set_xlabel('Temperature (℃)', fontsize=5)
88+
self.axes.set_ylabel('Abundances', fontsize=5)
89+
self.axes.legend(fontsize=4)
8990
self.draw()
9091

9192

@@ -109,8 +110,8 @@ def SingleTSAFigure(self, proteinData1, proteinData2, colNames, ProteinAccession
109110
self.axes.plot(temps_, meltCurve(temps_, paras2[0], paras2[1], paras2[2]))
110111

111112
self.axes.tick_params(labelsize=4)
112-
self.axes.set_xlabel('Temperature (℃)', fontsize=4)
113-
self.axes.set_ylabel('Abundances', fontsize=4)
113+
self.axes.set_xlabel('Temperature (℃)', fontsize=5)
114+
self.axes.set_ylabel('Abundances', fontsize=5)
114115
self.axes.legend(fontsize=3)
115116
self.draw()
116117

@@ -119,18 +120,18 @@ def RSDHistFigure(self, rsdList):
119120
rsdList = [i for i in rsdList if not np.isnan(i)]
120121
self.axes.cla()
121122
self.axes.hist(rsdList, 100)
122-
self.axes.tick_params(labelsize=3)
123-
self.axes.set_xlabel('RSD', fontsize=3)
124-
self.axes.set_ylabel('Number', fontsize=3)
123+
self.axes.tick_params(labelsize=4)
124+
self.axes.set_xlabel('RSD', fontsize=4)
125+
self.axes.set_ylabel('Number', fontsize=4)
125126
self.draw()
126127

127128

128129
def ROCFigure(self, fpr, tpr, auroc):
129130
self.axes.cla()
130131
self.axes.plot(fpr, tpr, label='AUC = {}'.format(auroc), color = 'red', lw=0.7)
131132
self.axes.plot([0, 1], [0, 1], color='black', linestyle='--', lw=0.7)
132-
self.axes.set_xlabel('False Positive Rate', fontsize = 4)
133-
self.axes.set_ylabel('True Positive Rate', fontsize = 4)
133+
self.axes.set_xlabel('False Positive Rate', fontsize = 5)
134+
self.axes.set_ylabel('True Positive Rate', fontsize = 5)
134135
self.axes.tick_params(labelsize=4)
135136
self.axes.legend(fontsize=3)
136137
self.draw()
@@ -156,8 +157,8 @@ def ProteinPairFigure(self, p1, p2, proteinData, colNames):
156157
self.axes.scatter(temps, vec, marker='.', label = p, s = 5)
157158
self.axes.plot(temps_, meltCurve(temps_, paras[0], paras[1], paras[2]), lw=1)
158159

159-
self.axes.set_xlabel('Temperature (℃)', fontsize=5)
160-
self.axes.set_ylabel('Abundances', fontsize=5)
160+
self.axes.set_xlabel('Temperature (℃)', fontsize=6)
161+
self.axes.set_ylabel('Abundances', fontsize=6)
161162
self.axes.legend(fontsize=4)
162163
self.draw()
163164

@@ -181,7 +182,7 @@ def iTSA_Volcano(self, iTSA_result, fc_thres, pv_thres):
181182
# sig = np.where(np.logical_and(np.abs(fc) >= np.log2(fc_thres), pv >= -np.log10(pv_thres)))[0]
182183

183184
self.axes.cla()
184-
scatterplot(data=pltdata, x="FC", y="PV", hue="G", palette='tab10', legend=False, alpha=0.9, marker='.', ax=self.axes)
185+
scatterplot(data=pltdata, x="FC", y="PV", hue="G", palette='tab10', legend=False, marker='.', alpha=0.7, edgecolor='none', ax=self.axes)
185186
'''
186187
markers = pltdata[pltdata['G'] == 'Both sig']
187188
markers = markers.iloc[:min(len(markers), 10),:]
@@ -197,8 +198,8 @@ def iTSA_Volcano(self, iTSA_result, fc_thres, pv_thres):
197198
self.axes.axvline(x = np.log2(fc_thres),ls = '--', color = 'black', lw=0.5)
198199
self.axes.axvline(x = -np.log2(fc_thres),ls = '--', color = 'black', lw=0.5)
199200
self.axes.axhline(y = -np.log10(pv_thres), ls = '--', color = 'black', lw=0.5)
200-
self.axes.set_xlabel('Log FC', fontsize = 4)
201-
self.axes.set_ylabel('-Log Adj P', fontsize = 4)
201+
self.axes.set_xlabel('Log FC', fontsize = 5)
202+
self.axes.set_ylabel('-Log Adj P', fontsize = 5)
202203
self.axes.tick_params(labelsize=4)
203204
self.draw()
204205

@@ -213,9 +214,9 @@ def PCAPlot(self, X, y):
213214
self.axes.cla()
214215
for i in range(len(label)):
215216
self.axes.scatter(X_r[y == label[i], 0], X_r[y == label[i], 1], alpha=.8, lw=1, label=target_names[i], s=10)
216-
self.axes.set_xlabel('PC 1', fontsize = 4)
217-
self.axes.set_ylabel('PC 2', fontsize = 4)
218-
self.axes.tick_params(labelsize=4)
217+
self.axes.set_xlabel('PC 1', fontsize = 5)
218+
self.axes.set_ylabel('PC 2', fontsize = 5)
219+
self.axes.tick_params(labelsize=5)
219220
self.draw()
220221

221222

@@ -225,8 +226,8 @@ def BarChart(self, X, y):
225226
flierprops = dict(markersize = 2)
226227
bplot = self.axes.boxplot(np.log2(X), patch_artist=True, flierprops=flierprops)
227228
self.axes.set_xticklabels(list(X.columns), rotation = 90)
228-
self.axes.set_xlabel('Sample', fontsize = 5)
229-
self.axes.set_ylabel('Log2 Intensity', fontsize = 5)
229+
self.axes.set_xlabel('Sample', fontsize = 6)
230+
self.axes.set_ylabel('Log2 Intensity', fontsize = 6)
230231
colors = [cm(val / len(X.columns)) for val in range(len(X.columns))]
231232
for patch, color in zip(bplot['boxes'], colors):
232233
patch.set_facecolor(color)
@@ -239,8 +240,8 @@ def CorrHeatMap(self, X):
239240
self.axes.imshow(corr, cmap="YlOrBr")
240241
self.axes.set_xticks(np.arange(corr.shape[0]))
241242
self.axes.set_yticks(np.arange(corr.shape[0]))
242-
self.axes.set_xticklabels(list(X.columns), fontsize = 5, rotation = 90)
243-
self.axes.set_yticklabels(list(X.columns), fontsize = 5)
243+
self.axes.set_xticklabels(list(X.columns), fontsize = 6, rotation = 90)
244+
self.axes.set_yticklabels(list(X.columns), fontsize = 6)
244245
for i in range(corr.shape[0]):
245246
for j in range(corr.shape[0]):
246247
self.axes.text(i, j, corr[i, j], ha="center", va="center", color="black", fontsize=3)
@@ -274,7 +275,7 @@ def TPP2D_Volcano(self, fdr_df, hits):
274275
# sig = np.where(np.logical_and(np.abs(fc) >= np.log2(fc_thres), pv >= -np.log10(pv_thres)))[0]
275276

276277
self.axes.cla()
277-
scatterplot(data=pltdata, x="x", y="y", hue="G", palette='tab10', legend=False, alpha=0.9, marker='.', ax=self.axes)
278+
scatterplot(data=pltdata, x="x", y="y", hue="G", palette='tab10', legend=False, alpha=0.7, edgecolor='none', marker='.', ax=self.axes)
278279
'''
279280
markers = pltdata[pltdata['G'] == 'Hits']
280281
markers = markers.iloc[:min(len(markers), 10),:]
@@ -287,8 +288,8 @@ def TPP2D_Volcano(self, fdr_df, hits):
287288
expand_points=(1, 1), expand_text=(1, 1),
288289
arrowprops=dict(arrowstyle="-", color='black', lw=0.5), ax=self.axes)
289290
'''
290-
self.axes.set_xlabel('sign(k) sqrt(RSS0-RSS1)', fontsize = 4)
291-
self.axes.set_ylabel('np.log2 (F_statistic + 1)', fontsize = 4)
291+
self.axes.set_xlabel('sign(k) sqrt(RSS0-RSS1)', fontsize = 5)
292+
self.axes.set_ylabel('np.log2 (F_statistic + 1)', fontsize = 5)
292293
self.axes.tick_params(labelsize=4)
293294
self.draw()
294295

@@ -305,8 +306,9 @@ def TPP2D_protHeatmap(self, data, ProteinAccession):
305306
img = pd.DataFrame(img)
306307
img.index = conc
307308
img.columns = temp
308-
heatmap(img, ax=self.axes)
309-
self.axes.set_xlabel('drug concentration', fontsize = 5)
310-
self.axes.set_ylabel('temperture', fontsize = 5)
309+
heatmap(img, ax=self.axes, cbar=False)
310+
self.axes.tick_params(labelsize = 6)
311+
self.axes.set_xlabel('temperture', fontsize = 6)
312+
self.axes.set_ylabel('drug concentration', fontsize = 6)
311313
self.draw()
312314

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