def PlotTTest2(XStart, XStop, Samp1, Samp2, Cov, PThr):
FileName1=os.path.split(Samp1)[1]
FileName1=os.path.splitext(FileName1)[0]
FileName2=os.path.split(Samp2)[1]
FileName2=os.path.splitext(FileName2)[0]
Samp1=Read(Samp1)
Samp2=Read(Samp2)
if Cov is not None:
Cov=Read(Cov)
if len(Cov.shape)==1:
Cov=Cov[:,np.newaxis]
Mean1=Samp1.mean(axis=0)
Mean2=Samp2.mean(axis=0)
delta=(XStop-XStart)/(Mean1.shape[0]-1)
if delta!=0:
X=np.arange(XStart, XStop+0.5*delta, delta)
else:
delta=1
XStart=1
XStop=Mean1.shape[0]
X=np.arange(Mean1.shape[0])
Ymax=np.max([Mean1, Mean2])
Ymin=np.min([Mean1, Mean2])
Ylimit=Ymax-Ymin
plt.ylim(Ymin-0.1*Ylimit, Ymax+0.5*Ylimit)
plt.xlim(XStart-delta, XStop+delta)
if PThr==0:
Leg1, Leg2=plt.plot(X, Mean1, 'kx-',
X, Mean2, 'kx--')
plt.legend((Leg1,Leg2),
(FileName1, FileName2))
else:
P=np.zeros_like(Mean1, dtype="bool")
for i in range(len(P)):
P[i]=ttest2(Samp1[i,:], Samp2[i,:], Cov)<PThr
if any(P==0):
Leg1, Leg2=plt.plot(X, Mean1, 'kx-',
X, Mean2, 'kx--')
plt.legend((Leg1,Leg2),
(FileName1, FileName2))
else:
YStar=np.max([Mean1, Mean2], axis=0)
XStar=X
YStar=YStar[P]
XStar=XStar[P]
Leg1, Leg2, Leg3=plt.plot(X, Mean1, 'kx-',
X, Mean2, 'kx--',
XStar, YStar, 'ks')
plt.legend((Leg1,Leg2,Leg3),
(FileName1, FileName2, 'p < %s' % str(PThr)))
plt.show()
def PlotCorr(Samp1, Samp2, Cov, PThr):
FileName1=os.path.split(Samp1)[1]
FileName1=os.path.splitext(FileName1)[0]
FileName2=os.path.split(Samp2)[1]
FileName2=os.path.splitext(FileName2)[0]
Samp1=Read(Samp1)
Samp2=Read(Samp2)
if Cov is not None:
Cov=Read(Cov)
if len(Cov.shape)==1:
Cov=Cov[:,np.newaxis]
Cov=np.concatenate(
(Cov, np.ones_like(Samp1)), axis=1)
b, Samp1, SSE=regress(Samp1, Cov)
b, Samp2, SSE=regress(Samp2, Cov)
b, intercept=np.polyfit(Samp1, Samp2, 1)
r=np.corrcoef(Samp1, Samp2)[0,1]
Line=b*Samp1+intercept
Xmax=Samp1.max()
Xmin=Samp1.min()
Ymax=np.max([Samp2, Line])
Ymin=np.min([Samp2, Line])
Xlimit=Xmax-Xmin
Ylimit=Ymax-Ymin
plt.plot(Samp1, Samp2, 'kx',
Samp1, Line, 'k-')
func="y=%.2fx+%.2f, r=%.2f" % (b, intercept, r)
plt.text(Xmax-0.2*Xlimit, Ymax+0.05*Ylimit,
'$%s$' % func)
plt.xlim(Xmin-0.1*Xlimit, Xmax+0.3*Xlimit)
plt.ylim(Ymin-0.1*Ylimit, Ymax+0.3*Ylimit)
plt.xlabel("X (Sample 1)")
plt.ylabel("Y (Sample 2)")
plt.show()
