def plot_2Dpmf(X, Y, xlabel, ylabel, title, saveas, bins=(100, 100)):
cubecmap.set_bad(color="lightgray", alpha=1.)
plt.figure()
z, x, y = np.histogram2d(X, Y, bins=bins)
F = -np.log(z)
F -= F.min()
extent = [x[0], x[-1], y[0], y[-1]]
F = np.ma.masked_invalid(F)
ax1 = plt.contourf(F.T, 100, extent=extent, cmap=cubecmap)
plt.xlabel(xlabel, fontsize=16)
plt.ylabel(ylabel, fontsize=16)
cbar = plt.colorbar()
cbar.ax.set_ylabel('Free energy (k$_B$T)', fontsize=15)
plt.title(title, fontsize=16)
if saveas is not None:
plt.savefig(saveas + ".png", bbox_inches="tight")
plt.savefig(saveas + ".pdf", bbox_inches="tight")
plt.savefig(saveas + ".eps", bbox_inches="tight")
def plot_2Dpmf(X,Y,xlabel,ylabel,title,saveas,bins=(100,100)):
cubecmap.set_bad(color="lightgray",alpha=1.)
plt.figure()
z,x,y = np.histogram2d(X,Y,bins=bins)
F = -np.log(z)
F -= F.min()
extent = [x[0], x[-1], y[0], y[-1]]
F = np.ma.masked_invalid(F)
ax1 = plt.contourf(F.T,100,extent=extent,cmap=cubecmap)
plt.xlabel(xlabel,fontsize=16)
plt.ylabel(ylabel,fontsize=16)
cbar = plt.colorbar()
cbar.ax.set_ylabel('Free energy (k$_B$T)',fontsize=15)
plt.title(title,fontsize=16)
if saveas is not None:
plt.savefig(saveas+".png",bbox_inches="tight")
plt.savefig(saveas+".pdf",bbox_inches="tight")
plt.savefig(saveas+".eps",bbox_inches="tight")
def plot_weights(C, coordname, title, saveas, shift):
C = np.ma.masked_invalid(C)
cubecmap.set_bad(color="lightgray", alpha=1.)
rwb = plt.get_cmap("bwr_r")
rwb.set_bad(color="lightgray", alpha=1.)
#shifted_cmap = shiftedColorMap(rwb, midpoint=shift, name='shifted')
plt.figure()
#plt.pcolormesh(C,cmap=cubecmap)
plt.pcolormesh(C, cmap=rwb, vmin=-0.1, vmax=0.1)
cbar = plt.colorbar()
cbar.ax.set_ylabel('Contact weight on %s' % coordname, fontsize=15)
plt.xlabel("Residue i", fontsize=16)
plt.ylabel("Residue j", fontsize=16)
plt.xlim(0, C.shape[0])
plt.ylim(0, C.shape[0])
plt.title(title, fontsize=16)
if saveas is not None:
plt.savefig(saveas + ".png", bbox_inches="tight")
plt.savefig(saveas + ".pdf", bbox_inches="tight")
plt.savefig(saveas + ".eps", bbox_inches="tight")
def plot_weights(C,coordname,title,saveas,shift):
C = np.ma.masked_invalid(C)
cubecmap.set_bad(color="lightgray",alpha=1.)
rwb = plt.get_cmap("bwr_r")
rwb.set_bad(color="lightgray",alpha=1.)
#shifted_cmap = shiftedColorMap(rwb, midpoint=shift, name='shifted')
plt.figure()
#plt.pcolormesh(C,cmap=cubecmap)
plt.pcolormesh(C,cmap=rwb,vmin=-0.1,vmax=0.1)
cbar = plt.colorbar()
cbar.ax.set_ylabel('Contact weight on %s' % coordname,fontsize=15)
plt.xlabel("Residue i",fontsize=16)
plt.ylabel("Residue j",fontsize=16)
plt.xlim(0,C.shape[0])
plt.ylim(0,C.shape[0])
plt.title(title,fontsize=16)
if saveas is not None:
plt.savefig(saveas+".png",bbox_inches="tight")
plt.savefig(saveas+".pdf",bbox_inches="tight")
plt.savefig(saveas+".eps",bbox_inches="tight")