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.