Dendrogram class #274
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@@ -105,3 +105,135 @@ def test_simple_streamline(self): | |
| self.assertListEqual(strln['data'][0]['x'][0:100], | ||
| expected_strln_0_100['x']) | ||
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| class TestDendrogram(TestCase): | ||
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| def test_default_dendrogram(self): | ||
| dendro = tls.FigureFactory.create_dendrogram(X=np.array([[1, 2, 3, 4], | ||
| [1, 1, 3, 4], | ||
| [1, 2, 1, 4], | ||
| [1, 2, 3, 1]])) | ||
| expected_data = [{'marker': {'color': 'rgb(255,133,27)'}, | ||
| 'mode': 'lines', 'xaxis': 'xs', | ||
| 'yaxis': 'y', | ||
| 'y': np.array([0., 1., 1., 0.]), | ||
| 'x': np.array([25., 25., 35., 35.]), | ||
| 'type': u'scatter'}, | ||
| {'marker': {'color': 'rgb(255,133,27)'}, | ||
| 'mode': 'lines', | ||
| 'xaxis': 'x', | ||
| 'yaxis': 'y', | ||
| 'y': np.array([0., 2.23606798, | ||
| 2.23606798, 1.]), | ||
| 'x': np.array([15., 15., 30., 30.]), | ||
| 'type': u'scatter'}, | ||
| {'marker': {'color': 'blue'}, | ||
| 'mode': 'lines', | ||
| 'xaxis': 'x', | ||
| 'yaxis': 'y', | ||
| 'y': np.array([0., 3.60555128, | ||
| 3.60555128, 2.23606798]), | ||
| 'x': np.array([5., 5., 22.5, 22.5]), | ||
| 'type': u'scatter'}] | ||
| expected_layout = {'width': '100%', | ||
| 'showlegend': False, | ||
| 'autoscale': False, | ||
| 'xaxis': {'showticklabels': True, | ||
| 'tickmode': 'array', | ||
| 'ticks': 'outside', | ||
| 'showgrid': False, | ||
| 'mirror': 'allticks', | ||
| 'zeroline': False, | ||
| 'showline': True, | ||
| 'ticktext': np.array(['3', '2', | ||
| '0', '1'], | ||
| dtype='|S1'), | ||
| 'rangemode': 'tozero', | ||
| 'type': 'linear', | ||
| 'tickvals': np.array([5.0, 15.0, | ||
| 25.0, 35.0])}, | ||
| 'yaxis': {'showticklabels': True, | ||
| 'ticks': 'outside', | ||
| 'showgrid': False, | ||
| 'mirror': 'allticks', | ||
| 'zeroline': False, | ||
| 'showline': True, | ||
| 'rangemode': 'tozero', | ||
| 'type': 'linear'}, | ||
| 'hovermode': 'closest'} | ||
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| # Make sure data is as expected | ||
| self.assertEqual(len(dendro['data']), len(expected_data)) | ||
| for i in range(1, len(dendro['data'])): | ||
| self.assertTrue(np.allclose(dendro['data'][i]['x'], | ||
| expected_data[i]['x'])) | ||
| self.assertTrue(np.allclose(dendro['data'][i]['y'], | ||
| expected_data[i]['y'])) | ||
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| # Make sure layout is as expected | ||
| self.assertTrue(np.array_equal(dendro['layout']['xaxis']['ticktext'], | ||
| expected_layout['xaxis']['ticktext'])) | ||
| self.assertTrue(np.array_equal(dendro['layout']['xaxis']['tickvals'], | ||
| expected_layout['xaxis']['tickvals'])) | ||
| self.assertEqual(dendro['layout']['xaxis']['ticks'], 'outside') | ||
| self.assertEqual(dendro['layout']['yaxis']['ticks'], 'outside') | ||
| self.assertEqual(dendro['layout']['width'], expected_layout['width']) | ||
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There was a problem hiding this comment. Can you also test that the output There was a problem hiding this comment. added layout test in ebff53e |
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| def test_dendrogram_random_matrix(self): | ||
| # create a random uncorrelated matrix | ||
| X = np.random.rand(5, 5) | ||
| # variable 2 is correlated with all the other variables | ||
| X[2, :] = sum(X, 0) | ||
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| names = ['Jack', 'Oxana', 'John', 'Chelsea', 'Mark'] | ||
| dendro = tls.FigureFactory.create_dendrogram(X, labels=names) | ||
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| # Check that 2 is in a separate cluster and it's labelled correctly | ||
| self.assertEqual(dendro['layout']['xaxis']['ticktext'][0], 'John') | ||
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| def test_dendrogram_orientation(self): | ||
| X = np.random.rand(5, 5) | ||
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| dendro_left = tls.FigureFactory.create_dendrogram( | ||
| X, orientation='left') | ||
| self.assertEqual(len(dendro_left['layout']['yaxis']['ticktext']), 5) | ||
| tickvals_left = np.array(dendro_left['layout']['yaxis']['tickvals']) | ||
| self.assertTrue((tickvals_left <= 0).all()) | ||
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| dendro_right = tls.FigureFactory.create_dendrogram( | ||
| X, orientation='right') | ||
| tickvals_right = np.array(dendro_right['layout']['yaxis']['tickvals']) | ||
| self.assertTrue((tickvals_right >= 0).all()) | ||
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| dendro_bottom = tls.FigureFactory.create_dendrogram( | ||
| X, orientation='bottom') | ||
| self.assertEqual(len(dendro_bottom['layout']['xaxis']['ticktext']), 5) | ||
| tickvals_bottom = np.array(dendro_bottom['layout']['xaxis']['tickvals']) | ||
| self.assertTrue((tickvals_bottom >= 0).all()) | ||
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| dendro_top = tls.FigureFactory.create_dendrogram(X, orientation='top') | ||
| tickvals_top = np.array(dendro_top['layout']['xaxis']['tickvals']) | ||
| self.assertTrue((tickvals_top <= 0).all()) | ||
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| def test_dendrogram_orientation(self): | ||
| X = np.array([[1, 2, 3, 4], | ||
| [1, 1, 3, 4], | ||
| [1, 2, 1, 4], | ||
| [1, 2, 3, 1]]) | ||
| greyscale = [ | ||
| 'rgb(0,0,0)', # black | ||
| 'rgb(05,105,105)', # dim grey | ||
| 'rgb(128,128,128)', # grey | ||
| 'rgb(169,169,169)', # dark grey | ||
| 'rgb(192,192,192)', # silver | ||
| 'rgb(211,211,211)', # light grey | ||
| 'rgb(220,220,220)', # gainsboro | ||
| 'rgb(245,245,245)'] # white smoke | ||
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| dendro = tls.FigureFactory.create_dendrogram(X, colorscale=greyscale) | ||
| self.assertEqual(dendro["data"][0]['marker']['color'], | ||
| 'rgb(128,128,128)') | ||
| self.assertEqual(dendro["data"][1]['marker']['color'], | ||
| 'rgb(128,128,128)') | ||
| self.assertEqual(dendro["data"][2]['marker']['color'], | ||
| 'rgb(0,0,0)') | ||
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Can you make sure that:
labelargument in works as expectedorientationin works as expectedcolorscalein works as expected. In particular, it's unclear if thecolorscaleused here is the same or different format from thecolorscaleused in Plotly JSON.It'd be best if these were tested separately to keep these unit tests from overlapping as much as possible.
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@theengineear right now the format of colorscale is different from plotly JSON, as is the goal of using it. Colorscale in this case only replaces default colors that scipy assigns to cluster elements. There is no control over to which element the color will be assigned as it is usually is with Plotly's colorscale key-value pairs.
Should I perhaps communicate this in a docstring/example?
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added a test 20fc40c