Principal component analysis in R | PCA for genetic diversity assessment using varimax rotation |

This video clearly explains the procedure involved in principal component analysis especially when we are using pca for genetic diversity assessment in plant breeding. Here you will understand why we need to do pca, how pca reduces dimensions, how to use rotation and how to interpret the graphs and results ?. In the core of this video you will find the syntax or the code which you need to run pca in R along with explanation for each and every argument explaining its importance with that i do show a lot of customisation options you need to follow in R to get beautiful, aesthetically appealing plots especially rotated component plot.

Reference Thesis
~ https://krishikosh.egranth.ac.in/disp...

For those who are interested in theory check out the articles below
~ PCA in R analyticsvidhya
https://www.analyticsvidhya.com/blog/...
~ PCA step by step
https://builtin.com/data-science/step...
~ PCA one stop shop
https://towardsdatascience.com/a-one-...
~ Learn PCA in 3d
https://setosa.io/ev/principal-compon...

In order to know about rotated component matrix please check the below article
~ Rotated component cross validated
https://stats.stackexchange.com/quest...

In order to know about the different functions of R
~ FactoMineR
http://factominer.free.fr/factomethod...
~ prcomp vs princomp
https://stats.stackexchange.com/quest....
~Add info
https://www.gastonsanchez.com/visuall...

00:00 Intro
05:46 Data structure in excel sheet
06:31 Beginner tips
07:11 Importing data
08:42 Scaling
10:36 Adjusting options
11:46 Visualisation packages
13:25 PCA-princomp
14:52 PCA-prcomp
20:46 3d plots
22:55 PCA-FactoMineR
34:04 Judging number of components
38:07 Elbow method
39:21 Rotated components

Script
https://docs.google.com/document/d/1W...
Dataset
https://docs.google.com/spreadsheets/...