Example: 08_plotting_validation_summary.py

[broadinstitute]

Example: 08_plotting_validation_summary.py

[joshua-gould]

Thanks. I updated compute_validation_summary to make day_pairs_triplets optional

[putnamdk]

I downloaded the updated file, Now I have this error: File “08_plotting_validation_summary.py”, line 15, in <module> vs = wot.commands.compute_validation_summary(ot_model) File optimal_transport_validation.py, line 44 in compute_validation_summary day_pairs_triplets.append((t0, t05, t1)) AttributeError: ‘NoneType’ object has no attribute ‘append’ Sincerely Daniel Putnam From: Joshua Gould <[email protected]> Reply-To: broadinstitute/wot <[email protected]> Date: Tuesday, February 12, 2019 at 10:06 AM To: broadinstitute/wot <[email protected]> Cc: Daniel Putnam <[email protected]>, Author <[email protected]> Subject: Re: [broadinstitute/wot] Example: 08_plotting_validation_summary.py (#28) Thanks. I updated compute_validation_summary to make day_pairs_triplets optional — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fbroadinstitute%2Fwot%2Fissues%2F28%23issuecomment-462820071&data=01%7C01%7Cdaniel.putnam%40stjude.org%7C4378a27131624279de1008d691040925%7C22340fa892264871b677d3b3e377af72%7C0&sdata=FJcJhGRiy6HrjCXXkzkNfYpi7zNivZyGyL5UcJdOml4%3D&reserved=0>, or mute the thread<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FABA26vu2L5UGAtZbNIa7Qu4lFCICxgrbks5vMuZ_gaJpZM4a23R1&data=01%7C01%7Cdaniel.putnam%40stjude.org%7C4378a27131624279de1008d691040925%7C22340fa892264871b677d3b3e377af72%7C0&sdata=TQszEMWnwcWpHO3FnGZm42j1mdavsK7%2FuMJPwKIY5kg%3D&reserved=0>.

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[joshua-gould]

Sorry, forgot to add day_pairs_triplets=[] to commit

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On Tue, Feb 12, 2019 at 11:41 AM Daniel Putnam ***@***.***> wrote: I downloaded the updated file, Now I have this error: File “08_plotting_validation_summary.py”, line 15, in <module> vs = wot.commands.compute_validation_summary(ot_model) File optimal_transport_validation.py, line 44 in compute_validation_summary day_pairs_triplets.append((t0, t05, t1)) AttributeError: ‘NoneType’ object has no attribute ‘append’ Sincerely Daniel Putnam From: Joshua Gould ***@***.***> Reply-To: broadinstitute/wot ***@***.***> Date: Tuesday, February 12, 2019 at 10:06 AM To: broadinstitute/wot ***@***.***> Cc: Daniel Putnam ***@***.***>, Author < ***@***.***> Subject: Re: [broadinstitute/wot] Example: 08_plotting_validation_summary.py (#28) Thanks. I updated compute_validation_summary to make day_pairs_triplets optional — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub< https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fbroadinstitute%2Fwot%2Fissues%2F28%23issuecomment-462820071&data=01%7C01%7Cdaniel.putnam%40stjude.org%7C4378a27131624279de1008d691040925%7C22340fa892264871b677d3b3e377af72%7C0&sdata=FJcJhGRiy6HrjCXXkzkNfYpi7zNivZyGyL5UcJdOml4%3D&reserved=0>, or mute the thread< https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FABA26vu2L5UGAtZbNIa7Qu4lFCICxgrbks5vMuZ_gaJpZM4a23R1&data=01%7C01%7Cdaniel.putnam%40stjude.org%7C4378a27131624279de1008d691040925%7C22340fa892264871b677d3b3e377af72%7C0&sdata=TQszEMWnwcWpHO3FnGZm42j1mdavsK7%2FuMJPwKIY5kg%3D&reserved=0>. ________________________________ Email Disclaimer: www.stjude.org/emaildisclaimer Consultation Disclaimer: www.stjude.org/consultationdisclaimer — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#28 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AE_pn-nK4qxKhUNLw3vXlYcD986KNoMbks5vMu7IgaJpZM4a23R1> .

[putnamdk]

I have made this update. Now, I see this error:

File “08_plotting_validation_summary.py”, line 15, in
vs = wot.commands.compute_validation_summary(ot_model)

File "../wot/commands/optimal_transport_validation.py", line 55 in compute_validation_summary
ot_model.compute_all_tansport_maps(with_covariates=True)

File "../wot/ot/ot_model.py", line 213, in compute_all_transport_maps
self.compute_transport_map(*x)

File "../wot/ot/ot_model.py", line 259, in compute_transport_map
tmap = OTModel.compute_single_transport_map(self.matrix, config)

File "../wot/ot/ot_model.py", line 336, in compute_single_transport_map
tmap = wot.ot.transport_stable_learn_growth(C, **config)
TypeError: transport_stable_learn_growth() got an unexpected keyword argument 'tmap_prefix'

[putnamdk]

I didn't mean to close the comment

[YubinXie]

TypeError: transport_stable_learn_growth() got an unexpected keyword argument 'tmap_prefix'
Same error here.

[joshua-gould]

Thanks, I updated the python code.