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Error with plot_topic
Hi all,
I try to run the tutorial but got this error. Would you have a suggestion?
To Reproduce plot_topic(cistopic_obj, reduction_name = 'UMAP', num_columns = 4)
Error output
ValueError Traceback (most recent call last)
Input In [45], in <cell line: 1>()
----> 1 plot_topic(cistopic_obj, reduction_name = 'UMAP', num_columns = 4)
File ~/pycisTopic/pycisTopic/clust_vis.py:728, in plot_topic(cistopic_obj, reduction_name, target, cmap, dot_size, alpha, scale, selected_topics, selected_features, harmony, figsize, num_columns, save)
726 scalarmappaple = cm.ScalarMappable(norm=normalize, cmap=cmap)
727 scalarmappaple.set_array(var_data)
--> 728 plt.colorbar(scalarmappaple)
729 if num_columns == 1:
730 if save is not None:
File ~/.local/lib/python3.9/site-packages/matplotlib/pyplot.py:2053, in colorbar(mappable, cax, ax, **kwargs)
2048 if mappable is None:
2049 raise RuntimeError('No mappable was found to use for colorbar '
2050 'creation. First define a mappable such as '
2051 'an image (with imshow) or a contour set ('
2052 'with contourf).')
-> 2053 ret = gcf().colorbar(mappable, cax=cax, ax=ax, **kwargs)
2054 return ret
File ~/.local/lib/python3.9/site-packages/matplotlib/figure.py:1256, in FigureBase.colorbar(self, mappable, cax, ax, use_gridspec, **kwargs)
1254 if cax is None:
1255 if ax is None:
-> 1256 raise ValueError(
1257 'Unable to determine Axes to steal space for Colorbar. '
1258 'Either provide the *cax* argument to use as the Axes for '
1259 'the Colorbar, provide the *ax* argument to steal space '
1260 'from it, or add *mappable* to an Axes.')
1261 current_ax = self.gca()
1262 userax = False
ValueError: Unable to determine Axes to steal space for Colorbar. Either provide the *cax* argument to use as the Axes for the Colorbar, provide the *ax* argument to steal space from it, or add *mappable* to an Axes.
Expected behavior 2022-08-05 09:17:31,790 cisTarget INFO Done! 2022-08-05 09:17:31,793 pycisTarget_wrapper INFO pbmc_tutorial/motifs/CTX_topics_otsu_No_promoters folder already exists. 2022-08-05 09:17:32,015 pycisTarget_wrapper INFO Running DEM for topics_otsu 2022-08-05 09:17:32,017 DEM INFO Reading DEM database
Version (please complete the following information):
- Python: [e.g. Python 3.9.12]
- SCENIC+: [e.g. 0.1.dev40+g4ff5053.d20210520]
Hi @Chrisdoan9
What is your matplotlib version?
All the best,
Seppe
Hi @SeppeDeWinter, it is 3.6.0. Thank you!
import matplotlib
matplotlib.__version__
Would you please have a look at this error which is more important? https://github.com/aertslab/scenicplus/issues/252
Hello, I'm facing the same problem and my matplotlib version is 3.8.0. Thanks.
Hi @JuanruMaryGuo. Have you run this cell? I have an error.
from scenicplus.wrappers.run_pycistarget import run_pycistarget
run_pycistarget(
region_sets = region_sets,
species = 'homo_sapiens',
save_path = os.path.join(work_dir, 'motifs'),
ctx_db_path = rankings_db,
dem_db_path = scores_db,
path_to_motif_annotations = motif_annotation,
run_without_promoters = True,
n_cpu = 8,
_temp_dir = os.path.join(tmp_dir, 'ray_spill'),
annotation_version = 'v10nr_clust',
)