Principal Component Analysis Question

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Andrew Orry

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Jan 12, 2023, 1:53:00 PM1/12/23
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Q. When using Principal Component Analysis in the Chemistry menu, can we have the components explicitly shown? Can we make a 3D plot of the components?

A.

1) Components are added as columns in the original table PC1, PC2, PC3

2) from the command line you can plot them in 3D using command line

Example: (assuming table name is Xdict)

# plot 3D using PC1,PC2,PC2 as X,Y,Z

 makeDataObj Xdict.PC1 Xdict.PC2 Xdict.PC3   

You can add color, radii and label if you have extra data.
In the example below it will use molLogP as color moWeight as radii and chemical name column as labels

 makeDataObj Xdict.PC1 Xdict.PC2 Xdict.PC3 Xdict.molLogP Xdict.molWeight Xdict.NAME_  "" "indigo/blue/green/yellow/orange/red"

it should produce something like the plot shown below

Labels are off by default. They can be toggled by atom label button (right click on plot and choose options) for all points or for selection only. 

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