Closed paul-hawkins closed 1 month ago
Hi Paul,
I am able to run your code snippet, on the data you uploaded.
I get this image.
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.
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. I ran the code of @paul-hawkins and I also obtained the same error. I have DABEST 0.3.0 as well. I am using Jupyter Notebook. Note that I can have a graph for only two variables: idx=('OMEGA','MOE'), the problem appears with more than two.
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.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ACCLAB/DABEST-python/issues/98#issuecomment-618349651, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AE6VZPUYO7EAMPJTNU4Q2NLROAROZANCNFSM4MMW7DAQ.
@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-hawkinshttps://github.com/paul-hawkins and @dhuzardhttps://github.com/dhuzard ,
This looks suspiciously like issues #67https://github.com/ACCLAB/DABEST-python/issues/67 and #70https://github.com/ACCLAB/DABEST-python/issues/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-hawkinshttps://github.com/paul-hawkins, I think upgrading pandas to >= 0.26 should do it. Can you give it a go?
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Apologies for this never being followed up with here. I hope all was sorted. I will close this issue for now, however, it can be reopened in the future if needed.
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