Worked Example: PCA on SNPs data from a vcf file Part 2 - Data Analysis

Introduction

The example is split into 2 Parts:

• Part 1: Data Preparation
• Part 2: Data analysis with PCA (this file)

Part 1 must be completed first to create a file, SNPs_cleaned.csv, that has been completely prepared for analysis.

Now in Part 2, you will analyze the data with PCA. The steps here will be:

1. Center the data (scale())
2. Run a PCA analysis (prcomp())
3. Evaluate the scree plot from the PCA (screeplot())
4. Evaluate the amount of variation explained by the first 2 PCs.
5. Extract the PCA scores for plotting (vegan::scores())
6. Plot the data

Tasks

In the code below all code is provided. Your tasks will be to do 4 things:

1. Give a meaningful title to all sections marked “TODO: TITLE”
2. Write 1 to 2 sentences describing what is being done and why in all sections marked “TODO: EXPLAIN”
3. Add titles and axes to plots in all sections marked “TODO: UPDATE PLOT”
4. Write 1 or 2 sentences interpreting the output from R in all sections marked “TODO: INTERPRET”

Preliminaries

Load the vcfR package with library()

library(vcfR) # KEY

## Warning: package 'vcfR' was built under R version 4.2.2

## 
##    *****       ***   vcfR   ***       *****
##    This is vcfR 1.13.0 
##      browseVignettes('vcfR') # Documentation
##      citation('vcfR') # Citation
##    *****       *****      *****       *****

library(vegan)

## Loading required package: permute

## Loading required package: lattice

## This is vegan 2.6-2

library(ggplot2)
library(ggpubr)

Set the working directory

Load the data

SNPs_cleaned <- read.csv(file = "SNPs_cleaned.csv")

warning("If this didn't work, its may be because you didn't set your working directory.")

## Warning: If this didn't work, its may be because you didn't set your working
## directory.

Data analysis

TODO: TITLE

TODO: EXPLAIN

SNPs_scaled <- scale(SNPs_cleaned)

TODO: TITLE

TODO: EXPLAIN

pca_scaled <- prcomp(SNPs_scaled)

TODO: TITLE

TODO: EXPLAIN

TODO: UPDATE PLOT WITH TITLE

screeplot(pca_scaled, 
          ylab  = "Relative importance",
          main = "give me a basic title")

TODO: INTERPRET SCREEPLOT

TODO: TITLE

TODO: EXPLAIN

summary_out_scaled <- summary(pca_scaled)

PCA_variation <- function(pca_summary, PCs = 2){
  var_explained <- pca_summary$importance[2,1:PCs]*100
  var_explained <- round(var_explained,1)
  return(var_explained)
}

var_out <- PCA_variation(summary_out_scaled,PCs = 10)

N_columns <- ncol(SNPs_scaled)
barplot(var_out,
        main = "Percent variation Scree plot",
        ylab = "Percent variation explained")
abline(h = 1/N_columns*100, col = 2, lwd = 2)

TODO: INTERPRET VARIANCE EXPLAINED

TODO: TITLE

TODO: EXPLAIN

biplot(pca_scaled)

TODO: EXPLAIN WHY THIS IS A BAD IDEA

TODO: TITLE

TODO: EXPLAIN

pca_scores <- vegan::scores(pca_scaled)

TODO: EXPLAIN

pop_id <- c("Nel","Nel","Nel","Nel","Nel","Nel","Nel","Nel",
"Nel", "Nel", "Nel", "Nel", "Nel", "Nel", "Nel", "Alt",
"Alt", "Alt", "Alt", "Alt", "Alt", "Alt", "Alt", "Alt",
"Alt", "Alt", "Alt", "Alt", "Alt", "Alt", "Sub", "Sub",
"Sub", "Sub", "Sub", "Sub", "Sub", "Sub", "Sub", "Sub",
"Sub", "Cau", "Cau", "Cau", "Cau", "Cau", "Cau", "Cau",
"Cau", "Cau", "Cau", "Cau", "Cau", "Div", "Div", "Div",
"Div", "Div", "Div", "Div", "Div", "Div", "Div", "Div",
"Div", "Div", "Div", "Div")

TODO: EXPLAIN

pca_scores2 <- data.frame(pop_id,
                              pca_scores)

TODO: TITLE

TODO: EXPLAIN

TODO: UPDATE PLOT WITH TITLE TODO: UPDATE X and Y AXES WITH AMOUNT OF VARIATION EXPLAINED

ggpubr::ggscatter(data = pca_scores2,
                  y = "PC2",
                  x = "PC1",
                  color = "pop_id",
                  shape = "pop_id",
                  xlab = "PC1 (xx% variation)",
                  ylab = "PC2 (xx% variation)",
                  main = "GIVE ME A TITLE")

TODO: INTERPRET PLOT