def test_ribbons():
N = 100
av = np.arange(N, dtype=np.int32) % 10
cp = circos.CircosPlot(av)
cp.set_entity_labels(["conn%d" % x for x in np.arange(N)])
cp.set_class_ribbons([(0, 4, 2), (7, 3, 2)])
circos.write(cp, 'ribbons.100.png', tempdir='plots')
def test_ribbons():
N = 100
av = np.arange(N, dtype=np.int32) % 10
cp = circos.CircosPlot(av)
cp.set_entity_labels(["conn%d" % x for x in np.arange(N)])
cp.set_class_ribbons([(0, 4, 2), (7, 3, 2)])
circos.write(cp, 'ribbons.100.png', tempdir='plots')
def test_multi_ribbons():
N = 100
av = np.arange(N, dtype=np.int32) % 10
cp = circos.CircosPlot(av)
cp.set_entity_labels(["conn%d" % x for x in np.arange(N)])
cp.add_class_ribbons([(0, 4, 2), (7, 3, 2)], 'red_a5')
cp.add_class_ribbons([(2, 3, 6), (1, 4, 4)], 'blue_a5')
circos.write(cp, 'ribbons.multi.100.png', tempdir='plots')
def test_multi_ribbons():
N = 100
av = np.arange(N, dtype=np.int32) % 10
cp = circos.CircosPlot(av)
cp.set_entity_labels(["conn%d" % x for x in np.arange(N)])
cp.add_class_ribbons([(0, 4, 2), (7, 3, 2)], 'red_a5')
cp.add_class_ribbons([(2, 3, 6), (1, 4, 4)], 'blue_a5')
circos.write(cp, 'ribbons.multi.100.png', tempdir='plots')
def test_both():
N = 100
av = np.arange(N, dtype=np.int32) % 10
cp = circos.CircosPlot(av)
cp.set_entity_labels(["conn%d" % x for x in np.arange(N)])
cp.set_entity_links(zip(np.random.permutation(N), np.random.permutation(N)))
cp.set_class_ribbons([(0, 4, 2), (7, 3, 4)])
circos.write(cp, 'both.100.png', tempdir='plots')
def test_simple():
# all one
av = np.zeros(100, dtype=np.int32)
cp = circos.CircosPlot(av)
circos.write(cp, 'allone.png', tempdir='plots')
av = np.arange(100, dtype=np.int32) % 10
cp = circos.CircosPlot(av)
circos.write(cp, 'many.png', tempdir='plots')
def test_both():
N = 100
av = np.arange(N, dtype=np.int32) % 10
cp = circos.CircosPlot(av)
cp.set_entity_labels(["conn%d" % x for x in np.arange(N)])
cp.set_entity_links(zip(np.random.permutation(N),
np.random.permutation(N)))
cp.set_class_ribbons([(0, 4, 2), (7, 3, 4)])
circos.write(cp, 'both.100.png', tempdir='plots')
def test_simple():
# all one
av = np.zeros(100, dtype=np.int32)
cp = circos.CircosPlot(av)
circos.write(cp, 'allone.png', tempdir='plots')
av = np.arange(100, dtype=np.int32) % 10
cp = circos.CircosPlot(av)
circos.write(cp, 'many.png', tempdir='plots')
def test_custom_colors():
# all one
av = np.arange(100, dtype=np.int32) % 10
custom_color_map = {'mycolor%d' % d : (255, d * 20 , 0) for d in range(10)}
cp = circos.CircosPlot(av,
karyotype_colors = ['mycolor%d' % d for d in range(10)],
custom_color_map = custom_color_map)
circos.write(cp, 'custom.colors.png', tempdir='plots')
def test_custom_colors():
# all one
av = np.arange(100, dtype=np.int32) % 10
custom_color_map = {'mycolor%d' % d: (255, d * 20, 0) for d in range(10)}
cp = circos.CircosPlot(
av,
karyotype_colors=['mycolor%d' % d for d in range(10)],
custom_color_map=custom_color_map)
circos.write(cp, 'custom.colors.png', tempdir='plots')
def test_heatmap_plot():
# all one
av = np.arange(100, dtype=np.int32) % 10
cp = circos.CircosPlot(av)
data_points = av
cp.add_plot('heatmap', {'r0' : '1.1r',
'r1' : '1.2r',
'min' : 0,
'max' : 10},
data_points,
)
circos.write(cp, 'plots.heatmap.png', tempdir='plots')
def test_scatter_plot():
# all one
av = np.arange(100, dtype=np.int32) % 10
cp = circos.CircosPlot(av)
data_points = av
cp.add_plot('scatter', {'r0' : '1.1r',
'r1' : '1.2r',
'min' : 0,
'max' : 10},
data_points,
{'backgrounds' : [('background', {'color': 'vvlgreen',
'y0' : 4,
'y1' : 8})]}
)
circos.write(cp, 'plots.scatter.png', tempdir='plots')
def test_heatmap_plot():
# all one
av = np.arange(100, dtype=np.int32) % 10
cp = circos.CircosPlot(av)
data_points = av
cp.add_plot(
'heatmap',
{
'r0': '1.1r',
'r1': '1.2r',
'min': 0,
'max': 10
},
data_points,
)
circos.write(cp, 'plots.heatmap.png', tempdir='plots')
def test_scatter_plot():
# all one
av = np.arange(100, dtype=np.int32) % 10
cp = circos.CircosPlot(av)
data_points = av
cp.add_plot('scatter', {
'r0': '1.1r',
'r1': '1.2r',
'min': 0,
'max': 10
}, data_points, {
'backgrounds': [('background', {
'color': 'vvlgreen',
'y0': 4,
'y1': 8
})]
})
circos.write(cp, 'plots.scatter.png', tempdir='plots')
def test_glyph_plot():
# all one
av = np.arange(300, dtype=np.int32) % 10
cp = circos.CircosPlot(av)
data_points = ["C" for d in av]
for i in range(0, 300, 7):
data_points[i] = 'A'
for i in range(0, 300, 4):
data_points[i] = 'L'
cp.add_plot(
'text', {
'r0': '1.05r',
'r1': '1.10r',
'label_size': '20p',
'label_font': 'glyph',
'label_rotate': 'yes',
}, data_points)
circos.write(cp, 'plots.glyphs.png', tempdir='plots')
def test_links():
N = 100
av = np.arange(N, dtype=np.int32) % 10
cp = circos.CircosPlot(av)
cp.set_entity_labels(["conn%d" % x for x in np.arange(N)])
cp.set_entity_links(zip(np.random.permutation(N), np.random.permutation(N)))
circos.write(cp, 'links.100.png', tempdir='plots')
N = 1000
av = np.arange(N, dtype=np.int32) % 10
cp = circos.CircosPlot(av)
cp.set_entity_labels(["conn%d" % x for x in np.arange(N)],
label_size="10p")
links = zip(np.random.permutation(N), np.random.permutation(N))
cp.set_entity_links(links[::10])
circos.write(cp, 'links.1000.svg', tempdir='plots')
def test_glyph_plot():
# all one
av = np.arange(300, dtype=np.int32) % 10
cp = circos.CircosPlot(av)
data_points = ["C" for d in av]
for i in range(0, 300, 7):
data_points[i]= 'A'
for i in range(0, 300, 4):
data_points[i]= 'L'
cp.add_plot('text', {'r0' : '1.05r',
'r1' : '1.10r',
'label_size' : '20p',
'label_font' : 'glyph',
'label_rotate' : 'yes',
},
data_points)
circos.write(cp, 'plots.glyphs.png', tempdir='plots')
def test_links():
N = 100
av = np.arange(N, dtype=np.int32) % 10
cp = circos.CircosPlot(av)
cp.set_entity_labels(["conn%d" % x for x in np.arange(N)])
cp.set_entity_links(zip(np.random.permutation(N),
np.random.permutation(N)))
circos.write(cp, 'links.100.png', tempdir='plots')
N = 1000
av = np.arange(N, dtype=np.int32) % 10
cp = circos.CircosPlot(av)
cp.set_entity_labels(["conn%d" % x for x in np.arange(N)],
label_size="10p")
links = zip(np.random.permutation(N), np.random.permutation(N))
cp.set_entity_links(links[::10])
circos.write(cp, 'links.1000.svg', tempdir='plots')
def test_labels():
av = np.arange(100, dtype=np.int32) % 10
cp = circos.CircosPlot(av)
cp.set_entity_labels(["conn%d" % x for x in np.arange(100)])
circos.write(cp, 'labels.png', tempdir='plots')
def test_labels():
av = np.arange(100, dtype=np.int32) % 10
cp = circos.CircosPlot(av)
cp.set_entity_labels(["conn%d" % x for x in np.arange(100)])
circos.write(cp, 'labels.png', tempdir='plots')
