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BINDetect - 'Annotation' object has no property 'text_from_points' only for time series #269

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sngholee opened this issue May 6, 2024 · 4 comments
Closed

BINDetect - 'Annotation' object has no property 'text_from_points' only for time series #269

sngholee opened this issue May 6, 2024 · 4 comments

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@sngholee
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sngholee commented May 6, 2024 •
edited by hschult
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Hello,

I'm getting this issue w/ BINDetct. I've tried downgrading adjusttext but still get this error message. This issue only arises when I do the time series, and running on single timepoints does not give any issues. I can't view the pdf output from the output when I try the time series. However, the other outputs (bindetect_results, bindetect_distances) seem fine. I'd appreciate any suggestions.

Code attempted:

TOBIAS BINDetect --motifs ${JASPAR} --signals ${BIGWIGS}/Lo_{0,2,24,48,72}_REP2_score.bw $i  --genome \ /public/groups/shariatilab/slee/RefGenomes/mm10.fa --peaks \ /public/groups/shariatilab/slee/MEKiRound3/ATACSeq/redo/consensusPeaks/consensusPeaksBEDCoordsOnly.txt \ --outdir ${OUTDIR}/ --time-series --cores 12

The error message:
Traceback (most recent call last): File "/public/home/slee393/miniconda3/bin/TOBIAS",
 line 33, in <module> sys.exit(load_entry_point('tobias==0.16.1', 'console_scripts', 'TOBIAS')()) 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
File "/public/home/slee393/miniconda3/lib/python3.11/site-packages/tobias-0.16.1-py3.11-linux-x86_64.egg/tobias/TOBIAS.py", 
line 162, in main args.func(args) 
^^^^^^^^^^^^^^^ 
File "/public/home/slee393/miniconda3/lib/python3.11/site-packages/tobias-0.16.1-py3.11-linux-x86_64.egg/tobias/tools/bindetect.py",
 line 819, in run_bindetect fig = plot_bindetect(motif_list, clustering, [cond1, cond2], args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
File "/public/home/slee393/miniconda3/lib/python3.11/site-packages/tobias-0.16.1-py3.11-linux-x86_64.egg/tobias/tools/bindetect_functions.py", 
line 773, in plot_bindetect adjust_text(txts, ax=ax1, add_objects=[l], text_from_points=True, arrowprops=dict(arrowstyle='-', color='black', lw=0.5))  #, expand_text=(0.1,1.2), expand_objects=(0.1,0.1)) 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
File "/public/home/slee393/miniconda3/lib/python3.11/site-packages/adjustText/__init__.py", 
line 730, in adjust_text ax.annotate(
 File "/public/home/slee393/miniconda3/lib/python3.11/site-packages/matplotlib/axes/_axes.py",
 line 711, in annotate a = mtext.Annotation(text, xy, xytext=xytext, xycoords=xycoords, 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
File "/public/home/slee393/miniconda3/lib/python3.11/site-packages/matplotlib/text.py",
 line 1845, in __init__ Text.__init__(self, x, y, text, **kwargs)
 File "/public/home/slee393/miniconda3/lib/python3.11/site-packages/matplotlib/text.py",
 line 155, in __init__ self.update(kwargs)
 File "/public/home/slee393/miniconda3/lib/python3.11/site-packages/matplotlib/text.py",
 line 205, in update ret.extend(super().update(kwargs)) 
^^^^^^^^^^^^^^^^^^^^^^ 
File "/public/home/slee393/miniconda3/lib/python3.11/site-packages/matplotlib/artist.py",
 line 1209, in update return self._update_props( 
^^^^^^^^^^^^^^^^^^^
 File "/public/home/slee393/miniconda3/lib/python3.11/site-packages/matplotlib/artist.py", 
line 1193, in _update_props raise AttributeError( AttributeError: 'Annotation' object has no property 'text_from_points'

Thank you
mohobein added a commit that referenced this issue May 21, 2024
@mohobein
fixed problems related to deprecated adjustText parameters #269 #259 etc
f7d1b05
mohobein added a commit that referenced this issue May 21, 2024
@mohobein
Merge pull request #270 from loosolab/adjustText-fix
99f7e27 
fixed problems related to deprecated adjustText parameters #269 #259 etc
@mohobein
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Hey @sngholee,

sorry for the late reply. I tried reproducing the error with the test data and was able to find a solution for it. The fix will be part of the next full release, but if you want to try it out already, you can install the dev branch via pip install git+https://github.com/loosolab/TOBIAS@dev. You might need to run pip install numpy cython in your environment beforehand.

I hope this fixes your problem. If not, we can look into it more closely.

Best regards,
Moritz

@sngholee
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Hello,

Thank you for looking into this. I tried installing the dev branch and reran the same code for time series, and got the below:

2024-05-22 15:17:14 (3017104) [INFO] Creating BINDetect plot(s) 2024-05-22 15:17:14 (3017104) [INFO] - Lo_0_REP2_score / Lo_2_REP2_score (static plot) Traceback (most recent call last): File "/public/home/slee393/miniconda3/bin/TOBIAS", line 8, in <module> sys.exit(main()) ^^^^^^ File "/public/home/slee393/miniconda3/lib/python3.11/site-packages/tobias/TOBIAS.py", line 162, in main args.func(args) ^^^^^^^^^^^^^^^ File "/public/home/slee393/miniconda3/lib/python3.11/site-packages/tobias/tools/bindetect.py", line 824, in run_bindetect fig = plot_bindetect(motif_list, clustering, [cond1, cond2], args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/public/home/slee393/miniconda3/lib/python3.11/site-packages/tobias/tools/bindetect_functions.py", line 776, in plot_bindetect adjust_text(txts, ax=ax1, objects=[l], arrowprops=dict(arrowstyle='-', color='black', lw=0.5)) #, expand_text=(0.1,1.2), expand_objects=(0.1,0.1)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/public/home/slee393/miniconda3/lib/python3.11/site-packages/adjustText/__init__.py", line 730, in adjust_text ax.annotate( File "/public/home/slee393/miniconda3/lib/python3.11/site-packages/matplotlib/axes/_axes.py", line 711, in annotate a = mtext.Annotation(text, xy, xytext=xytext, xycoords=xycoords, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/public/home/slee393/miniconda3/lib/python3.11/site-packages/matplotlib/text.py", line 1845, in __init__ Text.__init__(self, x, y, text, **kwargs) File "/public/home/slee393/miniconda3/lib/python3.11/site-packages/matplotlib/text.py", line 155, in __init__ self.update(kwargs) File "/public/home/slee393/miniconda3/lib/python3.11/site-packages/matplotlib/text.py", line 205, in update ret.extend(super().update(kwargs)) ^^^^^^^^^^^^^^^^^^^^^^ File "/public/home/slee393/miniconda3/lib/python3.11/site-packages/matplotlib/artist.py", line 1209, in update return self._update_props( ^^^^^^^^^^^^^^^^^^^ File "/public/home/slee393/miniconda3/lib/python3.11/site-packages/matplotlib/artist.py", line 1193, in _update_props raise AttributeError( AttributeError: 'Annotation' object has no property 'objects'

@mohobein
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mohobein commented May 23, 2024 •
edited
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My bad, I forgot to mention this. adjusttext is still downgraded in your environment from your earlier attempt at fixing it, right? The library changed multiple parameter names between versions, so with the newest TOBIAS version, you also need a version of adjusttext post these changes. Can you try updating adjusttext to the newest version and check if the issue persists? For me, it works with version 1.1.1.

@sngholee
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This worked, thank you!

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