Correction request in MINT sPLS-DA tutorial

[shaman-narayanasamy]

Dear authors,

I have been running the stemcells tutorial for MINT sPLS-DA. The code line plot(tune.mint, col = color.jet(2)) cannot be executed. I receive the following error:

Error in plot.tune.splsda(tune.mint, col = color.jet(2), sd = T) : object 'error.rate.sd' not found

The error was rectified when adding the sd = FALSE argument (i.e. plot(tune.mint, col = color.jet(2)), sd = T). However, the plot appears slightly different than the one shown in the tutorial (see uploaded image).

I hope that the tutorial can be corrected/updated such that newbies like myself do not get stuck. Please do not hesitate to contact me for more information

Best regards,
Shaman

[mixOmicsTeam]

Thanks Shaman, The website will be updated in the coming months and we will take a look at this sd error. Regards, Kim-Anh -- A/Prof. Kim-Anh Lê Cao NHMRC Career Development Fellow School of Mathematics and Statistics, Melbourne Integrative Genomics Bld 184 | The University of Melbourne T: +61 (0)3834 43971 | http://mixomics.org/ | http://lecao-lab.science.unimelb.edu.au/ | @mixOmics_team

…

________________________________ From: Shaman ***@***.***> Sent: Tuesday, November 30, 2021 10:08:37 PM To: mixOmicsTeam/mixOmics ***@***.***> Cc: Subscribed ***@***.***> Subject: [EXT] [mixOmicsTeam/mixOmics] Correction request in MING sPLS-DA tutorial (Issue #160) External email: Please exercise caution

________________________________ Dear authors, I have been running the stemcells tutorial for MINT sPLS-DA<http://mixomics.org/mixmint/stemcells-example>. The code line plot(tune.mint, col = color.jet(2)) cannot be executed. I receive the following error: Error in plot.tune.splsda(tune.mint, col = color.jet(2), sd = T) : object 'error.rate.sd' not found The error was rectified when adding the sd = FALSE argument (i.e. plot(tune.mint, col = color.jet(2)), sd = T). However, the plot appears slightly different than the one shown in the tutorial (see uploaded image). I hope that the tutorial can be corrected/updated such that newbies like myself do not get stuck. Please do not hesitate to contact me for more information Best regards, Shaman [image]<https://user-images.githubusercontent.com/4169854/144033607-876552aa-6b9a-4181-a3af-89e253f8bfa3.png> — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#160>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AJOK6LKXGMF3XXNJB7ABHZ3UOSWDHANCNFSM5JBQIW6A>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[shaman-narayanasamy]

Hi @mixOmicsTeam ,

Thank you for the response.

I found additional issues in the tutorial:

1. Same as issue plotArrow Error: Aesthetics must be either length 1 or the same as the data  #150

2. The cim plot (like the network plot) seems to be incompatible with Rstudio, perhaps the same comments in the network plot would be helpful for the learner, as the cim plot appears before the network plot.

 #save = 'jpeg',    #uncomment the following if you experience margin issues with RStudio 
 #name.save = network

[Max-Bladen]

Thank you very much @shaman-narayanasamy for these notes. In regards to all the issues you have raised with the MINT Stem Cells Case Study, they are all resolved now.

Please let me know if there's anything else you come across

[Max-Bladen]

@aljabadi If you could please close this issue when you get the chance, that'd be great thanks.