def plot(complex_lst):
## plot the cluster rmsd dist.
plot = biggles.FramedPlot()
inset = biggles.FramedPlot()
## plot title
plot.title = '/'.join(string.split(absfile(options['o']), '/')[-5:-1])
## customize plot appearence
plot.x1.label = 'cluster'
plot.y2.label = 'size'
plot.y1.label = 'rmsd'
plot.x2.draw_ticks = 0
plot.y2.draw_ticks = 0
inset.frame.draw_ticks = 0
inset.x1.draw_ticklabels = 0
inset.y1.draw_ticklabels = 0
inset.y2.draw_ticklabels = 1
inset.y2.draw_ticks = 1
inset.y2.ticks_style['color'] = 'red'
## get cluter and rmsd lists
clst_list = []
rms_list = []
for compl in complex_lst:
clst_list += [compl.info['hex_clst']]
rms_list += [compl.info['rms']]
## get average, max, min and size of cluster
data = []
clst_range = range(1, max(clst_list) + 1)
for clst in clst_range:
rms = compress(equal(clst_list, clst), rms_list)
data += [[average(rms), max(rms), min(rms), len(rms)]]
data = transpose(data)
## Inset
inset.add(biggles.Curve(clst_range, data[3], color='red'))
## Plot
plot.add(biggles.ErrorBarsY(clst_range, data[1], data[2]))
plot.add(biggles.Points(clst_range, data[0], type='cross', size=1))
plot.add(biggles.Inset((0.0, 0.0), (1.0, 1.0), inset))
plot.add(biggles.LineY(10, type='dot'))
## add label with info about 'good' solutions (average rmsd < 10A)
good = []
for clst in clst_range:
if data[0][clst - 1] < 10:
good += [clst]
plot.add(biggles.PlotLabel(0.5, 0.98, 'Solutions with rmsd < 10A', size=1))
plot.add(biggles.PlotLabel(0.5, 0.95, str(good), size=1))
## plot and save
plot.show()
plot.write_eps(string.split(options['o'], '.')[0] + '.eps')
def ramachandran(self):
"""
Create all the ramachandran plot points.
@return: list of biggles.Point objects (all the points of the
plot)and a biggles.Inset object (property scale).
@rtype: [ biggles.Point ], biggles.Inset
"""
p = []
## calculate colors and create a legend if a property is given
if self.profileName:
palette = CS('plasma', 0, 100)
col = palette.color_array(self.prof)
legend = Legend(palette.legend())
inset = biggles.Inset((1.1, 0.60), (1.2, .97), legend)
else:
col = ['black'] * len(self.phi)
inset = None
## add data points to plot
for i in range(len(self.phi)):
## don't add termini - has missing angles
if self.phi[i] and self.psi[i]:
if i in self.gly:
p += [
biggles.Point(self.psi[i],
self.phi[i],
type="star",
size=1,
color=col[i])
]
elif i in self.pro:
p += [
biggles.Point(self.psi[i],
self.phi[i],
type="filled square",
size=1,
color=col[i])
]
else:
p += [
biggles.Point(self.psi[i],
self.phi[i],
type="filled circle",
size=1,
color=col[i])
]
return p, inset
def __make_legend(self):
"""
Create and position the legend.
@return: biggles legend object
@rtype: biggles.Inset
"""
l = self.palette.legend()
legend = Legend(l)
inset = biggles.Inset((1.1, 0.60), (1.2, .97), legend)
return inset
def test_example4():
x = numpy.arange(0, 2 * numpy.pi, numpy.pi / 20)
s = numpy.sin(x)
inset = biggles.FramedPlot()
inset.title = "inset"
inset.frame.draw_ticks = 0
inset.add(biggles.Curve(x, s, type="dashed"))
p = biggles.FramedPlot()
p.aspect_ratio = 1.
p.frame.tickdir = +1
p.frame.draw_spine = 0
p.add(biggles.SymmetricErrorBarsY(x, s, [0.2] * len(x)))
p.add(biggles.Points(x, s, color="red"))
p.add(biggles.Inset((.6, .6), (.95, .95), inset))
_write_example(4, p)
biggles.configure('fontsize_min', 0.7)
for cg in cgList:
## path and name
cgFile = os.path.abspath(cg)
cgName = nameFromPath(cgFile)
print 'Working on ', cgName
## collect data
group = load(cgFile)
data, clst_range = clustInfo(group)
## create framedArray
plot = plotKey(data, cgName, 'fnrc_4.5')
plot.add(biggles.Inset((0.0, 0.0), (1.0, 1.0), plotClusterSize(data)))
plotList += [plot]
## gather cluster information
dist += clusterDist(data, cgName)
info += clusterInfo(data, cgName)
## grouping info
t2 = biggles.Table(1, 2)
stat1 = plotInfo(info)
stat2 = plotInfo(dist)
t2[0, 0] = stat2
t2[0, 1] = stat1
## add rfamedArrays to table
i = 0
inset.y2.draw_ticks = 0
dens = Biskit.hist.density(e_val[i], 25)
inset.add(
biggles.Curve(dens[:, 1],
dens[:, 0],
type='solid',
width=2,
color=spectrum[i]))
p_histogram += [inset]
## population lines
pop = [.2, .4, .6, .8]
popName = ['p2', 'p4', 'p6', 'p8']
for k in range(0, len(pop)):
popName[k] = biggles.LineY(populationDist(e_val[i], pop[k]),
type='dotted')
p_popLines += [popName]
## plot and save
for i in range(len(p_energy)):
p[i, 0].add(p_energy[i])
p[i, 0].add(p_label[i])
p[i, 0].add(p_average[i])
p[i, 0].add(p_reference[i])
p[i, 0].add(biggles.Inset((1.0, 0.00), (0.8, 1.0), p_histogram[i]))
for j in range(shape(p_popLines)[1]):
p[i, 0].add(p_popLines[i][j])
p.show()
p.write_eps(options['o'] + '/foldX_plot.eps', width="18cm", height="29cm")
#!/usr/bin/env python import sys sys.path.insert(1,'..') import biggles import math, numpy x = numpy.arange( 0, 2*math.pi, math.pi/20 ) s = numpy.sin(x) c = numpy.cos(x) inset = biggles.FramedPlot() inset.title = "inset" inset.frame.draw_ticks = 0 inset.add( biggles.Curve(x, s, type="dashed") ) p = biggles.FramedPlot() p.aspect_ratio = 1. p.frame.tickdir = +1 p.frame.draw_spine = 0 p.add( biggles.SymmetricErrorBarsY(x, s, [0.2]*len(x)) ) p.add( biggles.Points(x, s, color="red") ) p.add( biggles.Inset((.6,.6), (.95,.95), inset) ) #p.write_img( 400, 400, "example4.png" ) #p.write_eps( "example4.eps" ) p.show()
