LEfSe - Issue when plotting using the python script plot_res.py (Traceback (most recent call last)
Entering edit mode
17 months ago
Mania • 0

Hello everyone,

I am working on LEfSE, using data derived from qiime2 analysis (OTUs & numerical and categorical metadata in a number of samples and Iam trying to plot using lefse-plot_res.py without success. I ran the following commands but didn’t manage to obtain a plot… I am trying hard to fix issues mentioned in the output of the 3rd command and I would be thankful if help me do so!

My data is in this format input file

$ lefse-format_input.py collapse.table_FGF.txt tax-otu-table-form.txt -c 1 -u 2 -o 1000000

$ run_lefse.py tax-otu-table-form.txt tax-otu-table-result.txt

Terminal output: Number of significantly discriminative features: 16 ( 16 ) before internal wilcoxon Number of discriminative features with abs LDA score > 2.0 : 16

$ lefse-plot_res.py tax-otu-table-result.txt tax-otu-table-diffabund.pdf

Terminal output:

Traceback (most recent call last): File “/home/bigen2/miniconda3/envs/lefse/bin/lefse-plot_res.py”, line 177, in else: plot_histo_hor(params[‘output_file’],params,data,len(data[‘cls’]) == 2,params[‘report_features’]) File “/home/bigen2/miniconda3/envs/lefse/bin/lefse-plot_res.py”, line 70, in plot_histo_hor ax = fig.add_subplot(111,frame_on=False,axis_bgcolor=params[‘back_color’]) File “/home/bigen2/miniconda3/envs/lefse/lib/python2.7/site-packages/matplotlib/figure.py”, line 1257, in add_subplot a = subplot_class_factory(projection_class)(self, *args, kwargs) File “/home/bigen2/miniconda3/envs/lefse/lib/python2.7/site-packages/matplotlib/axes/_subplots.py”, line 77, in init self._axes_class.init(self, fig, self.figbox, kwargs) File “/home/bigen2/miniconda3/envs/lefse/lib/python2.7/site-packages/matplotlib/axes/_base.py”, line 541, in init self.update(kwargs) File “/home/bigen2/miniconda3/envs/lefse/lib/python2.7/site-packages/matplotlib/artist.py”, line 888, in update for k, v in props.items()] File “/home/bigen2/miniconda3/envs/lefse/lib/python2.7/site-packages/matplotlib/artist.py”, line 881, in _update_property raise AttributeError(‘Unknown property %s’ % k) AttributeError: Unknown property axis_bgcolor

Thank u in advance, Mania

metadata differentially taxa lefse abundant qiime2 numerical-categorical • 716 views
Entering edit mode
5 months ago

Did you find an answer to the issue? I am having the exact same issue. I would be really grateful if you identified a solution.

Entering edit mode

The cause of this problem might be matplotlib. Try to install within a new the lefse env a matplotlib version below 2.2.0



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