How can I interpret heat maps and Principale component analysis?

Question

[oshin707]

In the assignment I am doing we have two genotypes B and b. the assembly has two scaffolds and the aim is to test whether any part of the assembly is associated with B or b variants. And so we created heat maps and ran PCA on the genotypes. So we are suppose to analyse it and give summary statistics or a plot describing the patterns of differentiation.

Can any one please help me understand how to? I have never done it and am not familiar with it.

[natasha.sernova]

Some theory first:

ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap

http://nar.oxfordjournals.org/content/early/2015/05/12/nar.gkv468.full

The authors write about interpretation of both.

and this one:

http://biorxiv.org/content/biorxiv/early/2016/09/21/076463.full.pdf

shinyheatmap: ultra fast low memory heatmap software for big data genomics

[oshin707]

thank you so much for the links

[ddiez]

For PCA reading this question (and the answers) in CV may help. Currently, is the top question by votes raking!.