hmassalha
commented
1 year ago I am facing the same error when using my data, while it is not raise with the synthetic dataset.. any suggestions? thanks.
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ZeroDivisionError Traceback (most recent call last)
Input In [16], in <module>
4 # plt.setp(axes, xlim=custom_xlim, ylim=custom_ylim)
6 slingshot = Slingshot(data, cluster_labels_onehot, start_node=start_node, debug_level='verbose')
----> 8 slingshot.fit(num_epochs=2, debug_axes=axes)
File ~/my-conda-envs/sc_Harm/lib/python3.10/site-packages/slingshot/slingshot.py:135, in Slingshot.fit(self, num_epochs, debug_axes)
133 self._set_debug_axes(debug_axes)
134 if self.curves is None: # Initial curves and pseudotimes:
--> 135 self.get_lineages()
136 self.construct_initial_curves()
137 self.cell_weights = [self.cluster_labels_onehot[:, self.lineages[l].clusters].sum(axis=1)
138 for l in range(len(self.lineages))]
File ~/my-conda-envs/sc_Harm/lib/python3.10/site-packages/slingshot/slingshot.py:195, in Slingshot.get_lineages(self)
194 def get_lineages(self):
--> 195 tree = self.construct_mst(self.start_node)
197 # Determine lineages by parsing the MST
198 branch_clusters = deque()
File ~/my-conda-envs/sc_Harm/lib/python3.10/site-packages/slingshot/slingshot.py:123, in Slingshot.construct_mst(self, start_node)
121 # Plot clusters and MST
122 if self.debug_plot_mst:
--> 123 self.plotter.clusters(self.debug_axes[0, 0], alpha=0.5)
124 for root, kids in children.items():
125 for child in kids:
File ~/my-conda-envs/sc_Harm/lib/python3.10/site-packages/slingshot/plotter.py:77, in SlingshotPlotter.clusters(self, ax, labels, s, alpha, color_mode)
75 if color_mode == 'clusters':
76 colors = np.array(sns.color_palette('cubehelix', n_colors=sling.num_clusters))
---> 77 colors = generate_colormap(sling.num_clusters)
79 handles = [
80 Patch(color=colors.colors[k], label=labels[k]) for k in range(sling.num_clusters)
81 ]
82 ax.legend(handles=handles)
File ~/my-conda-envs/sc_Harm/lib/python3.10/site-packages/slingshot/plotter.py:48, in generate_colormap(number_of_distinct_colors)
46 lower_half = lower_partitions_half * number_of_shades
47 for i in range(3):
---> 48 initial_cm[0:lower_half, i] *= np.arange(0.2, 1, 0.8/lower_half)
50 # Modify second half in such way that colours towards end of partition are less intense and brighter
51 # Colours closer to the middle are affected less, colours closer to the end are affected more
52 for i in range(3):
ZeroDivisionError: float division by zero
Sometimes happens. Don't know why. https://github.com/mossjacob/pyslingshot/blob/master/slingshot/plotter.py#L48