I am using matplotlib to create a graph for my thesis. I am using the following code:
import numpy as np
import numpy as np
import matplotlib as mpl
mpl.use('pgf')
fig_width_pt = 390 # Get this from LaTeX using \showthe\columnwidth
inches_per_pt = 1.0/72.27 # Convert pt to inch
golden_mean = (np.sqrt(5)-1.0)/2.0 # Aesthetic ratio
fig_width = fig_width_pt*inches_per_pt # width in inches
fig_height = fig_width*golden_mean # height in inches
fig_size = [fig_width,fig_height]
pgf_with_latex = { # setup matplotlib to use latex for output
"pgf.texsystem": "pdflatex", # change this if using xetex or lautex
"text.usetex": True, # use LaTeX to write all text
"font.family": "serif",
"font.serif": [], # blank entries should cause plots to inherit fonts from the document
"font.sans-serif": [],
"font.monospace": [],
"axes.labelsize": 10, # LaTeX default is 10pt font.
"text.fontsize": 10,
"legend.fontsize": 8, # Make the legend/label fonts a little smaller
"xtick.labelsize": 8,
"ytick.labelsize": 8,
"figure.figsize": fig_size,
'axes.linewidth': .5,
'lines.linewidth': .5,
'patch.linewidth': .5,
"pgf.preamble": [
r"\usepackage[utf8x]{inputenc}", # use utf8 fonts becasue your computer can handle it :)
]
}
mpl.rcParams.update(pgf_with_latex)
import matplotlib.mlab as mlab
import matplotlib.pyplot as plt
import colorsys
def savefig(filename):
plt.savefig('{}.pgf'.format(filename))
plt.savefig('{}.pdf'.format(filename))
# setup
title = 'Clustering after salting out'
ylabel = '% of total colloids'
xlabel = 'Cluster size'
xticklabels = ('1','2','3','4','5','6','7','5+')
legend = ['10min', '20min','30min']
# read data from files
# skipped this part for legibility
# calculations with data, skipped for legibility
# plot it in a bar plot
N = len(ys[0])
ind = np.arange(0, N+1, 1.2) # the x locations for the groups
width = 0.35 # the width of the bars
# generate colours
hsv_colours = [(x*1.0/N, 0.8, 0.8) for x in range(N)]
rgb_colours = map(lambda x: colorsys.hsv_to_rgb(*x), hsv_colours)
fig, ax = plt.subplots()
rects = [ax.bar([x+i*width for x in ind], y, width, color=rgb_colours[i], yerr=errors_percentage[i]) for i,y in enumerate(ys)]
# add some info
ax.set_ylabel(ylabel)
ax.set_xlabel(xlabel)
ax.set_title(title)
ax.set_xticks(ind+width)
ax.set_xticklabels(xticklabels)
ax.axis([0,7,0,60])
ax.legend(rects, legend)
savefig('tpm_cluster_statistics')
The output produced looks like this:
As you can see, the last bar of the bar plot is not totally filled. Do I need some other setting to get it working? The goal is to create a PGF file for inclusion in a LaTex document. The PDF file is just for previewing. The partially filled bar is both in the PDF and in the PGF file. Any help is greatly appreciated!
Edit: In reply to tcaswell: this is a minimum working example that you can try on your computer:
import numpy as np
import numpy as np
import matplotlib as mpl
mpl.use('pgf')
pgf_with_latex = { # setup matplotlib to use latex for output
"pgf.texsystem": "pdflatex", # change this if using xetex or lautex
"text.usetex": True, # use LaTeX to write all text
}
mpl.rcParams.update(pgf_with_latex)
import matplotlib.mlab as mlab
import matplotlib.pyplot as plt
import colorsys
def savefig(filename):
plt.savefig('{}.pgf'.format(filename))
plt.savefig('{}.pdf'.format(filename))
# setup
title = 'Title'
ylabel = 'x'
xlabel = 'y'
xticklabels = ('1','2','3','4','5','6','7','8')
legend = ['1', '2','3']
#data
ys = [[51.63593099345628, 28.911362284354553, 12.135633551457465, 4.521118381915526, 1.189767995240928, 0.7138607971445567, 0.41641879833432477, 0.4759071980963712], [46.66359871145882, 21.445006902899216, 14.496088357109988, 7.363092498849516, 4.1417395306028535, 3.313391624482283, 0.0, 2.577082374597331], [52.642595499738356, 22.39665096807954, 12.087912087912088, 7.744636316064887, 2.3547880690737837, 1.5698587127158554, 0.3663003663003663, 0.837257980115123]]
# plot it in a bar plot
N = len(ys[0])
ind = np.arange(0, N+1, 1.2) # the x locations for the groups
width = 0.35 # the width of the bars
fig, ax = plt.subplots()
rects = [ax.bar([x+i*width for x in ind], y, width) for i,y in enumerate(ys)]
# add some info
ax.set_ylabel(ylabel)
ax.set_xlabel(xlabel)
ax.set_title(title)
ax.set_xticks(ind+width)
ax.set_xticklabels(xticklabels)
ax.axis([0,7,0,60])
ax.legend(rects, legend)
savefig('tpm_cluster_statistics')
Then the result looks like this:
But when I remove these lines:
mpl.use('pgf')
pgf_with_latex = { # setup matplotlib to use latex for output
"pgf.texsystem": "pdflatex", # change this if using xetex or lautex
"text.usetex": True, # use LaTeX to write all text
}
mpl.rcParams.update(pgf_with_latex)
And just show the output using plt.show(), the result does look correct.
