PCoA Code

Required Packages

#library(dplyr)
#require(graphics)
library(ggplot2)
library(ggfortify)
library(plotly)

## 
## Attaching package: 'plotly'

## The following object is masked from 'package:ggplot2':
## 
##     last_plot

## The following object is masked from 'package:stats':
## 
##     filter

## The following object is masked from 'package:graphics':
## 
##     layout

#setting seed ensures PC1/2 values will be consistent across uses
set.seed(100)

Preparing the Distance Matrix

#set working directory
#replace the distance matrix file with either "Shh", "Sox2", or "Hoxb1Distancematrix.csv"
df <- read.csv("~/Desktop/bio321hw/ShhDistanceMatrix.csv") #Shh will be our example

#replace NA values with 0
df[is.na(df)] = 0

#Make species row names and remove unnecessary column with "X***"
df <- as.matrix(df[,-1])
row.names(df) <- colnames(df)

• At this point, the data format would be verified with “head” or “View()”

Using ggplot2 and ggfortify/plotly to generate PCoA

#run PCoA analysis with default parameters - "scale. = T" says the variables should be scaled 
pcoa_Shh <- prcomp(df,scale. = T)
Shh <- autoplot(pcoa_Shh,shape = F, label = T,)
Shh + labs(title = "Shh PCoA Analysis")