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Problem with plotting mean_diff #98
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Hi @josesho , I have the same issue with my data: an "IndexError: index 10 is out of bounds for size 8" when running the plot function. |
That’s very odd, as I am using 0.3.0 too.
Paul.
From: Joses W. Ho <notifications@github.com>
Sent: Thursday, April 23, 2020 5:33 AM
To: ACCLAB/DABEST-python <DABEST-python@noreply.github.com>
Cc: Paul Hawkins <phawkins@eyesopen.com>; Author <author@noreply.github.com>
Subject: Re: [ACCLAB/DABEST-python] Problem with plotting mean_diff (#98)
Hi Paul,
I am able to run your code snippet, on the data you uploaded.
Can I check: what is your DABEST version when you run
dabest.__version___
or
db.__version___
given than you import DABEST as db in your example? I'm using the latest version, DABEST v0.3.0.
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@paul-hawkins and @dhuzard , This looks suspiciously like issues #67 and #70. Could I trouble both of you to check what version of pandas you two have installed? import pandas as pd
pd.__version__ Thanks! |
I found out the solution: upgrading to python 3.8 ! |
Hi Joses,
'0.25.3'
Does updating to Python 3.8 fix the issue, as dhuzard suggested?
Paul.
From: Joses W. Ho <notifications@github.com>
Sent: Friday, April 24, 2020 1:33 AM
To: ACCLAB/DABEST-python <DABEST-python@noreply.github.com>
Cc: Paul Hawkins <phawkins@eyesopen.com>; Mention <mention@noreply.github.com>
Subject: Re: [ACCLAB/DABEST-python] Problem with plotting mean_diff (#98)
@paul-hawkins<https://github.com/paul-hawkins> and @dhuzard<https://github.com/dhuzard> ,
This looks suspiciously like issues #67<#67> and #70<#70>.
Could I trouble both of you to check what version of pandas you two have installed?
import pandas as pd
pd.__version__
Thanks!
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Hi, @paul-hawkins, I think upgrading pandas to >= 0.26 should do it. Can you give it a go? |
Upon upgrading to pandas 1.0.3 I saw this
(oepython36) C:\Users\phawkins>pip install --upgrade pandas
Collecting pandas
Downloading https://files.pythonhosted.org/packages/d2/81/a1514c993ad8261a2053f356c3ea9a6ad41871a09a8ef9cf46789e371a63/pandas-1.0.3-cp36-cp36m-win_amd64.whl (8.7MB)
|████████████████████████████████| 8.7MB 819kB/s
Requirement already satisfied, skipping upgrade: python-dateutil>=2.6.1 in c:\users\phawkins\anaconda3\envs\oepython36\lib\site-packages (from pandas) (2.8.0)
Requirement already satisfied, skipping upgrade: numpy>=1.13.3 in c:\users\phawkins\anaconda3\envs\oepython36\lib\site-packages (from pandas) (1.17.2)
Requirement already satisfied, skipping upgrade: pytz>=2017.2 in c:\users\phawkins\anaconda3\envs\oepython36\lib\site-packages (from pandas) (2019.2)
Requirement already satisfied, skipping upgrade: six>=1.5 in c:\users\phawkins\anaconda3\envs\oepython36\lib\site-packages (from python-dateutil>=2.6.1->pandas) (1.12.0)
ERROR: dabest 0.3.0 has requirement pandas!=0.25.2,~=0.25, but you'll have pandas 1.0.3 which is incompatible.
Installing collected packages: pandas
Found existing installation: pandas 0.25.1
Uninstalling pandas-0.25.1:
Successfully uninstalled pandas-0.25.1
Successfully installed pandas-1.0.3
(oepython36) C:\Users\phawkins>
However, as you said, upgrading works! (albeit with a warning)
C:\Users\phawkins\Anaconda3\envs\oepython36\lib\site-packages\IPython\core\pylabtools.py:128: UserWarning: This figure includes Axes that are not compatible with tight_layout, so results might be incorrect. fig.canvas.print_figure(bytes_io, **kw)
[cid:image001.png@01D61C84.2FCFB2D0]
One last thing – how do I change the font size in the violin plot and the distribution plot? I see I can pass in ‘violinplot_kwargs’ but
violinplot_kwargs={'fontsize':36})
does not work. I can’t see how to go about changing the distribution plot at all.
Thanks for all the help Joses,
Paul.
From: Joses W. Ho <notifications@github.com>
Sent: Sunday, April 26, 2020 9:19 PM
To: ACCLAB/DABEST-python <DABEST-python@noreply.github.com>
Cc: Paul Hawkins <phawkins@eyesopen.com>; Mention <mention@noreply.github.com>
Subject: Re: [ACCLAB/DABEST-python] Problem with plotting mean_diff (#98)
Hi, @paul-hawkins<https://github.com/paul-hawkins>, I think upgrading pandas to >= 0.26 should do it. Can you give it a go?
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The following code should produce two plots, but only the swarm plot is produced, and an error is thrown.
new_df = pd.read_csv('%s/all_ringrmsd_data_only.txt' % rootdir, sep='\t')
s_control = db.load(new_df,idx=('OMEGA','MOE','Macromodel','Desmond','RDKit','Prime'))
s_control.cohens_d
s_control.mean_diff.plot(raw_marker_size=3)
IndexError: index 12 is out of bounds for size 12
all_ringrmsd_data_only.txt
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