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gkichaev / PAINTOR_V3.0

Fast, integrative fine mapping with functional data
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Error with CANVIS #63

Closed jinghuazhao closed 1 year ago

jinghuazhao commented 1 year ago

I am running CANVIS under Python 2.7.18 with the following problem,

python CANVIS.py -l chr4.3473139.rs6831256.post.filt.300 -z ldl.Zscore tg.Zscore -r chr4.3473139.rs6831256.ld.filt.300 -a chr4.3473139.rs6831256.annot.filt.300 -s E066.H3K27ac.narrowPeak.Adult_Liver E066.H3K4me1.narrowPeak.Adult_Liver -t 99 -i 3381705 3507346

... first complaints about .as_matrix should be .values() go away when changing to .to_numpy()

Traceback (most recent call last): File "CANVIS.py", line 518, in main() File "CANVIS.py", line 492, in main zscore_plots = Plot_Statistic_Value(location, zscores, zscore_names, greyscale, ld) File "CANVIS.py", line 124, in Plot_Statistic_Value sub = fig.add_subplot(1,1,1, axisbg='white') File "/usr/local/Cluster-Apps/ceuadmin/PAINTOR/3.0/CANVIS/lib/python2.7/site-packages/matplotlib/figure.py", line 1257, in add_subplot a = subplot_class_factory(projection_class)(self, *args, kwargs) File "/usr/local/Cluster-Apps/ceuadmin/PAINTOR/3.0/CANVIS/lib/python2.7/site-packages/matplotlib/axes/_subplots.py", line 77, in init self._axes_class.init(self, fig, self.figbox, kwargs) File "/usr/local/Cluster-Apps/ceuadmin/PAINTOR/3.0/CANVIS/lib/python2.7/site-packages/matplotlib/axes/_base.py", line 541, in init self.update(kwargs) File "/usr/local/Cluster-Apps/ceuadmin/PAINTOR/3.0/CANVIS/lib/python2.7/site-packages/matplotlib/artist.py", line 888, in update for k, v in props.items()] File "/usr/local/Cluster-Apps/ceuadmin/PAINTOR/3.0/CANVIS/lib/python2.7/site-packages/matplotlib/artist.py", line 881, in _update_property raise AttributeError('Unknown property %s' % k) AttributeError: Unknown property axisbg

Any suggestions?

ruthjohnson95 commented 1 year ago

Hi Jing Hua,

Could you also copy the error/warning regarding the ".as_matrix" message?

-- Ruth D. Johnson PhD Student Dept of Computer Science University of California, Los Angeles @.***

On Fri, Nov 11, 2022 at 11:59 AM Jing Hua Zhao @.***> wrote:

I am running CANVIS under Python 2.7.18 with the following problem,

python CANVIS.py -l chr4.3473139.rs6831256.post.filt.300 -z ldl.Zscore tg.Zscore -r chr4.3473139.rs6831256.ld.filt.300 -a chr4.3473139.rs6831256.annot.filt.300 -s E066.H3K27ac.narrowPeak.Adult_Liver E066.H3K4me1.narrowPeak.Adult_Liver -t 99 -i 3381705 3507346

... first complaints about .as_matrix should be .values() go away when changing to .to_numpy()

Traceback (most recent call last): File "CANVIS.py", line 518, in main() File "CANVIS.py", line 492, in main zscore_plots = Plot_Statistic_Value(location, zscores, zscore_names, greyscale, ld) File "CANVIS.py", line 124, in Plot_Statistic_Value sub = fig.add_subplot(1,1,1, axisbg='white') File "/usr/local/Cluster-Apps/ceuadmin/PAINTOR/3.0/CANVIS/lib/python2.7/site-packages/matplotlib/figure.py", line 1257, in add_subplot a = subplot_class_factory(projection_class)(self, *args, kwargs) File "/usr/local/Cluster-Apps/ceuadmin/PAINTOR/3.0/CANVIS/lib/python2.7/site-packages/matplotlib/axes/_subplots.py", line 77, in init self._axes_class.init(self, fig, self.figbox, kwargs) File "/usr/local/Cluster-Apps/ceuadmin/PAINTOR/3.0/CANVIS/lib/python2.7/site-packages/matplotlib/axes/_base.py", line 541, in init self.update(kwargs) File "/usr/local/Cluster-Apps/ceuadmin/PAINTOR/3.0/CANVIS/lib/python2.7/site-packages/matplotlib/artist.py", line 888, in update for k, v in props.items()] File "/usr/local/Cluster-Apps/ceuadmin/PAINTOR/3.0/CANVIS/lib/python2.7/site-packages/matplotlib/artist.py", line 881, in _update_property raise AttributeError('Unknown property %s' % k) AttributeError: Unknown property axisbg

Any suggestions?

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jinghuazhao commented 1 year ago

Sure. This is the message from run_canvis.sh CANVIS.py:69: FutureWarning: Method .as_matrix will be removed in a future version. Use .values instead. ld_matrix = ld.as_matrix() CANVIS.py:85: FutureWarning: Method .as_matrix will be removed in a future version. Use .values instead. annotations = annotations.as_matrix() CANVIS.py:89: FutureWarning: Method .as_matrix will be removed in a future version. Use .values instead. zscores = zscores.as_matrix() CANVIS.py:91: FutureWarning: Method .as_matrix will be removed in a future version. Use .values instead. pos_prob = pos_prob.as_matrix() CANVIS.py:93: FutureWarning: Method .as_matrix will be removed in a future version. Use .values instead. location = location.as_matrix() Traceback (most recent call last): File "CANVIS.py", line 518, in main() File "CANVIS.py", line 492, in main zscore_plots = Plot_Statistic_Value(location, zscores, zscore_names, greyscale, ld) File "CANVIS.py", line 124, in Plot_Statistic_Value sub = fig.add_subplot(1,1,1, axisbg='white') File "/usr/local/Cluster-Apps/ceuadmin/PAINTOR/3.0/CANVIS/lib/python2.7/site-packages/matplotlib/figure.py", line 1257, in add_subplot a = subplot_class_factory(projection_class)(self, *args, kwargs) File "/usr/local/Cluster-Apps/ceuadmin/PAINTOR/3.0/CANVIS/lib/python2.7/site-packages/matplotlib/axes/_subplots.py", line 77, in init self._axes_class.init(self, fig, self.figbox, kwargs) File "/usr/local/Cluster-Apps/ceuadmin/PAINTOR/3.0/CANVIS/lib/python2.7/site-packages/matplotlib/axes/_base.py", line 541, in init self.update(kwargs) File "/usr/local/Cluster-Apps/ceuadmin/PAINTOR/3.0/CANVIS/lib/python2.7/site-packages/matplotlib/artist.py", line 888, in update for k, v in props.items()] File "/usr/local/Cluster-Apps/ceuadmin/PAINTOR/3.0/CANVIS/lib/python2.7/site-packages/matplotlib/artist.py", line 881, in _update_property raise AttributeError('Unknown property %s' % k) AttributeError: Unknown property axisbg

ruthjohnson95 commented 1 year ago

Thanks for the information.

It looks like the numpy .as_matrix() message is only a warning and that the main error is from matplotlib. Can you confirm that you have the correct matplotlib versions listed in the Github?

According to a preliminary search, this is the source of the error:

https://stackoverflow.com/questions/50504053/attributeerror-unknown-property-axisbg

The code base is pretty straightforward, so you might be able to just implement the change listed in the StackOverflow post if you don't want to fiddle with the versions.

-- Ruth D. Johnson PhD Student Dept of Computer Science University of California, Los Angeles @.***

On Sat, Nov 12, 2022 at 1:07 AM Jing Hua Zhao @.***> wrote:

Sure. This is the message from run_canvis.sh CANVIS.py:69: FutureWarning: Method .as_matrix will be removed in a future version. Use .values instead. ld_matrix = ld.as_matrix() CANVIS.py:85: FutureWarning: Method .as_matrix will be removed in a future version. Use .values instead. annotations = annotations.as_matrix() CANVIS.py:89: FutureWarning: Method .as_matrix will be removed in a future version. Use .values instead. zscores = zscores.as_matrix() CANVIS.py:91: FutureWarning: Method .as_matrix will be removed in a future version. Use .values instead. pos_prob = pos_prob.as_matrix() CANVIS.py:93: FutureWarning: Method .as_matrix will be removed in a future version. Use .values instead. location = location.as_matrix() Traceback (most recent call last): File "CANVIS.py", line 518, in main() File "CANVIS.py", line 492, in main zscore_plots = Plot_Statistic_Value(location, zscores, zscore_names, greyscale, ld) File "CANVIS.py", line 124, in Plot_Statistic_Value sub = fig.add_subplot(1,1,1, axisbg='white') File "/usr/local/Cluster-Apps/ceuadmin/PAINTOR/3.0/CANVIS/lib/python2.7/site-packages/matplotlib/figure.py", line 1257, in add_subplot a = subplot_class_factory(projection_class)(self, *args, kwargs) File "/usr/local/Cluster-Apps/ceuadmin/PAINTOR/3.0/CANVIS/lib/python2.7/site-packages/matplotlib/axes/_subplots.py", line 77, in init self._axes_class.init(self, fig, self.figbox, kwargs) File "/usr/local/Cluster-Apps/ceuadmin/PAINTOR/3.0/CANVIS/lib/python2.7/site-packages/matplotlib/axes/_base.py", line 541, in init self.update(kwargs) File "/usr/local/Cluster-Apps/ceuadmin/PAINTOR/3.0/CANVIS/lib/python2.7/site-packages/matplotlib/artist.py", line 888, in update for k, v in props.items()] File "/usr/local/Cluster-Apps/ceuadmin/PAINTOR/3.0/CANVIS/lib/python2.7/site-packages/matplotlib/artist.py", line 881, in _update_property raise AttributeError('Unknown property %s' % k) AttributeError: Unknown property axisbg

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jinghuazhao commented 1 year ago

Thanks. I now follow specifications from wiki with a requirements.txt, so that 'pip freeze' gives me

cycler==0.10.0 functools32==3.2.3.post2 lxml==4.9.1 matplotlib==2.0.0 numpy==1.12.0 pandas==0.15.2 pyparsing==2.4.7 python-dateutil==2.8.2 pytz==2022.6 scipy==0.15.1 seaborn==0.7.1 six==1.16.0 subprocess32==3.5.4 svgutils==0.3.4

It does indicate facecolor option but another complaint.

/usr/local/Cluster-Apps/ceuadmin/PAINTOR/3.0/CANVIS/lib/python2.7/site-packages/matplotlib/cbook.py:136: MatplotlibDeprecationWarning: The axisbg attribute was deprecated in version 2.0. Use facecolor instead. warnings.warn(message, mplDeprecation, stacklevel=1) Traceback (most recent call last): File "CANVIS.py", line 518, in main() File "CANVIS.py", line 505, in main Assemble_Figure(zscore_plots, value_plots, heatmap, annotation_plot, output, horizontal) File "CANVIS.py", line 364, in Assemble_Figure plot4.moveto(0,y_scale, scale=1.40) TypeError: moveto() got an unexpected keyword argument 'scale'

ruthjohnson95 commented 1 year ago

Ah I see. Can you downgrade your svgutils to "svgutils==0.2.0". I believe the error stems from this.

-- Ruth D. Johnson PhD Student Dept of Computer Science University of California, Los Angeles @.***

On Sun, Nov 13, 2022 at 2:46 PM Jing Hua Zhao @.***> wrote:

Thanks. I now follow specifications from wiki with a requirements.txt, so that 'pip freeze' gives me

cycler==0.10.0 functools32==3.2.3.post2 lxml==4.9.1 matplotlib==2.0.0 numpy==1.12.0 pandas==0.15.2 pyparsing==2.4.7 python-dateutil==2.8.2 pytz==2022.6 scipy==0.15.1 seaborn==0.7.1 six==1.16.0 subprocess32==3.5.4 svgutils==0.3.4

It does indicate facecolor option but another complaint.

/usr/local/Cluster-Apps/ceuadmin/PAINTOR/3.0/CANVIS/lib/python2.7/site-packages/matplotlib/cbook.py:136: MatplotlibDeprecationWarning: The axisbg attribute was deprecated in version 2.0. Use facecolor instead. warnings.warn(message, mplDeprecation, stacklevel=1) Traceback (most recent call last): File "CANVIS.py", line 518, in main() File "CANVIS.py", line 505, in main Assemble_Figure(zscore_plots, value_plots, heatmap, annotation_plot, output, horizontal) File "CANVIS.py", line 364, in Assemble_Figure plot4.moveto(0,y_scale, scale=1.40) TypeError: moveto() got an unexpected keyword argument 'scale'

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jinghuazhao commented 1 year ago

Hi Ruth,

I just returned to this and indeed with svgutils 0.2.0 the script runs successfully.

Kind regards,

Jing Hua

ruthjohnson95 commented 1 year ago

Great! I'm glad this got resolved. I'll update the readme to explicitly list the version for svgutils.

-- Ruth D. Johnson PhD Student Dept of Computer Science University of California, Los Angeles @.***

On Thu, Nov 17, 2022 at 12:20 PM Jing Hua Zhao @.***> wrote:

Hi Ruth,

I just returned to this and indeed with svgutils 0.2.0 the script runs successfully.

Kind regards,

Jing Hua

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