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#/usr/bin/env python
from cogent.draw.multivariate_plot import (plot_ordination,
map_colors, text_points, scatter_points, plot_points, arrows)
from cogent.util.unit_test import TestCase, main
import os, pylab
from tempfile import mkstemp
from numpy import asarray, c_
from pdb import set_trace
__author__ = "Rob Knight"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Rob Knight"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Rob Knight"
__email__ = "rob@spot.colorado.edu"
__status__ = "Production"
######
# util class
class TestCasePlot(TestCase):
Debug = True
def fig(self, fname=None):
if self.Debug:
pylab.show()
else:
if not fname:
fd, fname = mkstemp(prefix='PlotTest_', suffix='.png')
pylab.savefig(fname)
pylab.clf()
os.remove(fname)
def p(self, obj):
if self.Debug:
print obj
class TestI(TestCasePlot):
def setUp(self):
self.points = [(0, 0), (1,1), (1,2), (2, 2)]
#adjust canvas
#pylab.xlim(-0.5, 2.5)
#pylab.ylim(-0.5, 2.5)
class FunctionsTests(TestI):
def test_map_colors(self):
#default
self.assertEqual(map_colors(range(3)),
['#000080', '#7dff7a', '#800000'])
#alternative cmap
self.assertEqual(map_colors(range(3), cmap='hot'),
['#0b0000', '#ff5c00', '#ffffff'])
#return tuples
self.assertFloatEqual(map_colors(range(3), mode='tuples'),
[(0.0, 0.0, 0.5), (0.490196, 1.0, 0.477546), (0.5, 0.0, 0.0)])
def test_text_points(self):
#same text for all the points
text_points(self.points, 'X')
self.fig()
def test_text_points_diff_texts(self):
#diff text for all the points
text_points(self.points, ['A', 'B', 'C', 'A'])
self.fig()
def test_plot_points(self):
plot_points(self.points, label='X')
self.fig()
class scatter_points_tests(TestI):
def test_basic(self):
scatter_points(self.points, label='X')
self.fig()
def test_color_list(self):
scatter_points(self.points, c=['k', 'red', '#00FF00', (0, 0, 1)],
s=[100, 200, 300, 400], marker=['o', 's', 'd', 'h'])
pylab.xlim(-0.5, 2.5)
pylab.ylim(-0.5, 2.5)
self.fig()
def test_color_shades(self):
#self.Debug = True
scatter_points(self.points, c=[1, 2, 3, 4],
s=[100, 200, 300, 400], marker=['o', 's', 'd', 'h'])
pylab.xlim(-0.5, 2.5)
pylab.ylim(-0.5, 2.5)
self.fig()
class arrows_tests(TestI):
def test_arrows(self):
points = self.points
arrows([[0,0]]*len(points), points)
self.fig()
class plot_ordination_tests(TestCasePlot):
def setUp(self):
self.points = points_3d
self.keys = ['eigvals', 'samples', 'species', 'centroids', 'biplot']
self.values = [
[0.3, 0.1, 0, -0.5], #eigvals
self.points, #samples
self.points + 0.2, #species
[(0, 1, 0), (2, -2, 0)], #centroids
[(0.5, 0.5, 1), (-1, 1.5, 1)], #biplot
]
def test_basic(self):
res = dict(zip(self.keys[:2], self.values))
plot_ordination(res)
self.fig()
def test_species(self):
res = dict(zip(self.keys[:3], self.values))
plot_ordination(res)
self.fig()
def test_centroids(self):
res = dict(zip(self.keys[:4], self.values))
plot_ordination(res)
self.fig()
def test_biplot(self):
res = dict(zip(self.keys, self.values))
plot_ordination(res,
species_kw={'label': 'sp'}, biplot_kw={'label':['b1', 'b2']},
samples_kw={'label': 'sa'})
self.fig()
def test_choices(self):
res = dict(zip(self.keys, self.values))
plot_ordination(res, choices=[2,3])
self.fig()
def test_axis_names(self):
#self.Debug = True
res = dict(zip(self.keys[:2], self.values))
plot_ordination(res, axis_names=['CCA1', 'CA1', 'CA2'],
constrained_names='CCA')
self.fig()
#####
# test data
points = asarray([(0,0), (-1, 1), (1, -2), (2, 3)], float)
points_3d = c_[points, [[3]]*len(points)]
if __name__ == '__main__':
main()
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