plotting example: plot_2d_spectrum

This example shows how to use nmrglue and matplotlib to create figures for examining data or publication. In this example a contour plot of the spectrum from a 2D NMRPipe file is created. Slices are added in the 15N and 13C dimension as well as sample peak labels. plotting example: plot_2d_spectrum_pts is similar to this example but plotted on a point scale.

[source code]

#! /usr/bin/env python
# Create contour plots of a 2D NMRPipe spectrum

import nmrglue as ng
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.cm

# plot parameters
cmap = matplotlib.cm.Blues_r    # contour map (colors to use for contours)
contour_start   = 30000     # contour level start value
contour_num     = 20        # number of contour levels
contour_factor  = 1.20      # scaling factor between contour levels

# calculate contour levels
cl = [contour_start*contour_factor**x for x in xrange(contour_num)]

# read in the data from a NMRPipe file
dic,data = ng.pipe.read("../../common_data/2d_pipe/test.ft2")

# make ppm scales
uc_13c = ng.pipe.make_uc(dic,data,dim=1)
ppm_13c = uc_13c.ppm_scale()
#ppm_13c = np.linspace(uc_13c.ppm(0),uc_13c.ppm(data.shape[1]-1),data.shape[1])
uc_15n = ng.pipe.make_uc(dic,data,dim=0)
ppm_15n = uc_15n.ppm_scale()
#ppm_15n = np.linspace(uc_15n.ppm(0),uc_15n.ppm(data.shape[0]-1),data.shape[0])

# create the figure
fig = plt.figure()
ax = fig.add_subplot(111)

# plot the contours
etup = (ppm_13c[0],ppm_13c[-1],ppm_15n[0],ppm_15n[-1])
ax.contour(data,cl,cmap=cmap,extent=etup)

# add some labels
ax.text(59.25,104.0,"T49",size=8,color='r')
ax.text(58.75,106,"T11",size=8,color='k')

# plot slices in each direction
xslice = data[uc_15n("111.27 ppm"),:]
ax.plot(ppm_13c,-xslice/4.e4+111.27)
yslice = data[:,uc_13c("62.0 ppm")]
ax.plot(yslice/2.e4+62.0,ppm_15n)

# decorate the axes
ax.set_ylabel("15N (ppm)")
ax.set_xlabel("13C (ppm)")
ax.set_title("Protein 2D NCa Spectrum")
ax.set_xlim(70,40)
ax.set_ylim(135,100)

# save the figure
fig.savefig("spectrum.png") # change to .pdf, .ps, etc for different formats

Result:

[spectrum.png]