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Thank you for this wonderfull tool.
I am running a Single-methylome analysis, everything goes well. preprocess, correlation, ordinal, metagene, grouping with boxplot...but when running grouping violinplot an error is produced:
python grouping.py -n WDM -p violinplot
Traceback (most recent call last):
File "grouping.py", line 217, in
main()
File "grouping.py", line 211, in main
groupingplot(All_value,name, plot=args.plot, context=con, target=tar, skip0=eval(args.skip0), n=args.numberofgroup,showmeans=eval(args.showmeans),showfliers=eval(args.showfliers),ylim=args.ylimit,corr=args.correlation,figuresize=(8,6),dotsize=args.dotsize,textsize=args.textsize,ticksize=args.ticksize,labelsize=args.labelsize,titlesize=args.titlesize)
File "grouping.py", line 140, in groupingplot
plt.violinplot(dataforplot,showmeans=showmeans)
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/matplotlib/pyplot.py", line 3737, in violinplot
points=points, bw_method=bw_method, data=data)
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/matplotlib/init.py", line 1870, in inner
return func(ax, *args, **kwargs)
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/matplotlib/axes/_axes.py", line 7958, in violinplot
vpstats = cbook.violin_stats(dataset, _kde_method, points=points)
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/matplotlib/cbook/init.py", line 2183, in violin_stats
stats['vals'] = method(x, coords)
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/matplotlib/axes/_axes.py", line 7953, in _kde_method
if np.all(X[0] == X):
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/pandas/core/series.py", line 868, in getitem
result = self.index.get_value(self, key)
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/pandas/core/indexes/base.py", line 4375, in get_value
tz=getattr(series.dtype, 'tz', None))
File "pandas/_libs/index.pyx", line 81, in pandas._libs.index.IndexEngine.get_value
File "pandas/_libs/index.pyx", line 89, in pandas._libs.index.IndexEngine.get_value
File "pandas/_libs/index.pyx", line 132, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 987, in pandas._libs.hashtable.Int64HashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 993, in pandas._libs.hashtable.Int64HashTable.get_item
KeyError: 0
(METHGET) yomismo@onuba:/media/yomismo/Datos/MethGET$ python grouping.py -n MDM -p violinplot
Traceback (most recent call last):
File "grouping.py", line 217, in
main()
File "grouping.py", line 211, in main
groupingplot(All_value,name, plot=args.plot, context=con, target=tar, skip0=eval(args.skip0), n=args.numberofgroup,showmeans=eval(args.showmeans),showfliers=eval(args.showfliers),ylim=args.ylimit,corr=args.correlation,figuresize=(8,6),dotsize=args.dotsize,textsize=args.textsize,ticksize=args.ticksize,labelsize=args.labelsize,titlesize=args.titlesize)
File "grouping.py", line 140, in groupingplot
plt.violinplot(dataforplot,showmeans=showmeans)
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/matplotlib/pyplot.py", line 3737, in violinplot
points=points, bw_method=bw_method, data=data)
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/matplotlib/init.py", line 1870, in inner
return func(ax, *args, **kwargs)
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/matplotlib/axes/_axes.py", line 7958, in violinplot
vpstats = cbook.violin_stats(dataset, _kde_method, points=points)
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/matplotlib/cbook/init.py", line 2183, in violin_stats
stats['vals'] = method(x, coords)
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/matplotlib/axes/_axes.py", line 7953, in _kde_method
if np.all(X[0] == X):
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/pandas/core/series.py", line 868, in getitem
result = self.index.get_value(self, key)
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/pandas/core/indexes/base.py", line 4375, in get_value
tz=getattr(series.dtype, 'tz', None))
File "pandas/_libs/index.pyx", line 81, in pandas._libs.index.IndexEngine.get_value
File "pandas/_libs/index.pyx", line 89, in pandas._libs.index.IndexEngine.get_value
File "pandas/_libs/index.pyx", line 132, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 987, in pandas._libs.hashtable.Int64HashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 993, in pandas._libs.hashtable.Int64HashTable.get_item
KeyError: 0
I have checked all dependencies and are ok
Thank you for your help
The text was updated successfully, but these errors were encountered:
Thank you for this wonderfull tool.
I am running a Single-methylome analysis, everything goes well. preprocess, correlation, ordinal, metagene, grouping with boxplot...but when running grouping violinplot an error is produced:
python grouping.py -n WDM -p violinplot
Traceback (most recent call last):
File "grouping.py", line 217, in
main()
File "grouping.py", line 211, in main
groupingplot(All_value,name, plot=args.plot, context=con, target=tar, skip0=eval(args.skip0), n=args.numberofgroup,showmeans=eval(args.showmeans),showfliers=eval(args.showfliers),ylim=args.ylimit,corr=args.correlation,figuresize=(8,6),dotsize=args.dotsize,textsize=args.textsize,ticksize=args.ticksize,labelsize=args.labelsize,titlesize=args.titlesize)
File "grouping.py", line 140, in groupingplot
plt.violinplot(dataforplot,showmeans=showmeans)
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/matplotlib/pyplot.py", line 3737, in violinplot
points=points, bw_method=bw_method, data=data)
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/matplotlib/init.py", line 1870, in inner
return func(ax, *args, **kwargs)
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/matplotlib/axes/_axes.py", line 7958, in violinplot
vpstats = cbook.violin_stats(dataset, _kde_method, points=points)
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/matplotlib/cbook/init.py", line 2183, in violin_stats
stats['vals'] = method(x, coords)
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/matplotlib/axes/_axes.py", line 7953, in _kde_method
if np.all(X[0] == X):
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/pandas/core/series.py", line 868, in getitem
result = self.index.get_value(self, key)
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/pandas/core/indexes/base.py", line 4375, in get_value
tz=getattr(series.dtype, 'tz', None))
File "pandas/_libs/index.pyx", line 81, in pandas._libs.index.IndexEngine.get_value
File "pandas/_libs/index.pyx", line 89, in pandas._libs.index.IndexEngine.get_value
File "pandas/_libs/index.pyx", line 132, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 987, in pandas._libs.hashtable.Int64HashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 993, in pandas._libs.hashtable.Int64HashTable.get_item
KeyError: 0
(METHGET) yomismo@onuba:/media/yomismo/Datos/MethGET$ python grouping.py -n MDM -p violinplot
Traceback (most recent call last):
File "grouping.py", line 217, in
main()
File "grouping.py", line 211, in main
groupingplot(All_value,name, plot=args.plot, context=con, target=tar, skip0=eval(args.skip0), n=args.numberofgroup,showmeans=eval(args.showmeans),showfliers=eval(args.showfliers),ylim=args.ylimit,corr=args.correlation,figuresize=(8,6),dotsize=args.dotsize,textsize=args.textsize,ticksize=args.ticksize,labelsize=args.labelsize,titlesize=args.titlesize)
File "grouping.py", line 140, in groupingplot
plt.violinplot(dataforplot,showmeans=showmeans)
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/matplotlib/pyplot.py", line 3737, in violinplot
points=points, bw_method=bw_method, data=data)
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/matplotlib/init.py", line 1870, in inner
return func(ax, *args, **kwargs)
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/matplotlib/axes/_axes.py", line 7958, in violinplot
vpstats = cbook.violin_stats(dataset, _kde_method, points=points)
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/matplotlib/cbook/init.py", line 2183, in violin_stats
stats['vals'] = method(x, coords)
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/matplotlib/axes/_axes.py", line 7953, in _kde_method
if np.all(X[0] == X):
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/pandas/core/series.py", line 868, in getitem
result = self.index.get_value(self, key)
File "/home/yomismo/mambaforge/envs/METHGET/lib/python2.7/site-packages/pandas/core/indexes/base.py", line 4375, in get_value
tz=getattr(series.dtype, 'tz', None))
File "pandas/_libs/index.pyx", line 81, in pandas._libs.index.IndexEngine.get_value
File "pandas/_libs/index.pyx", line 89, in pandas._libs.index.IndexEngine.get_value
File "pandas/_libs/index.pyx", line 132, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 987, in pandas._libs.hashtable.Int64HashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 993, in pandas._libs.hashtable.Int64HashTable.get_item
KeyError: 0
I have checked all dependencies and are ok
Thank you for your help
The text was updated successfully, but these errors were encountered: