| what parameters shall be used to create t-SNE or PCA visualization in Data Warrior [message #1524] |
Fri, 04 March 2022 00:15  |
yi02@hotmail.com
Messages: 1
Registered: March 2022
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Junior Member |
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Hi, there:
I am new to chemoinformatics, and I tried to create t-SNE visualization with Data Warrior for a group of compounds that I tried to see if any patterns or classes formed amongst them. I did Data->Create t-SNE Visualization, and then choose Structure [FragFp] amongst a list of potential parameters offered from the dropdown list. I saw other options such as cLogP,cLogS, H-Acceptors etc, are those potential or good parameters to be used for t-SNE or PCA visualization? Shall I try each of them? Or, Is there other features or structure descriptors we can used to create t-SNE and/or PCA? and is there a way for us to create such structure descriptors or parameters in Data Warrior?
Thanks so much in advance!
Best
Mike
[Updated on: Sat, 05 March 2022 07:05] Report message to a moderator |
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| Re: what parameters shall be used to create t-SNE or PCA visualization in Data Warrior [message #1575 is a reply to message #1524] |
Sat, 02 April 2022 17:28  |
thomas
Messages: 715
Registered: June 2014
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Senior Member |
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Hi Mike,
t-SNE or PCA are usually done with lots of parameters, which is either one chemical descriptor (if it is a vector) or many numerical criteria. For instance, these could be inhibition values on many targets. Among the descriptors the SkelSpheres should be the best option, because is represents chemical structure similarity better the the simpler and faster binary descriptors. Descriptors can be added to a file with 'Chemistry->From Chemical Structure->Calculate Descriptor->...
Thomas
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