CODEWITHSUNDEEP
rdataframe
Angels Vásquez
Angels Vásquez

Reputation: 11

Creating a dataframe in R using two datasets

I have two datasets, and I need to create a dataframe that allows me to select one column for each data set, and create a boxplot. For instance, one dataset has information about Treatment, and the other dataset has a Shannon diversity index measurement

library(ggplot2)
library(vegan)
library(tidyverse)

# This code will create a matrix with 30 columns representing species and 10 rows representing communities.
# The object will be called "community_matrix"

set.seed(2)
community1=matrix(
  sample(0:250,300,replace=T),nrow=10,
  dimnames=list(paste("community",1:10,sep=""),paste("sp",1:30,sep="")))
community2=matrix(
  sample(50:200,300,replace=T),nrow=10,
  dimnames=list(paste("community",11:20,sep=""),paste("sp",1:30,sep="")))
community_matrix<- rbind(community1,community2)

#This code will create a metadata table depicting the treatments.

m1<- as.data.frame(list(paste("community",1:10,sep=""), paste("T1")))
colnames(m1)<- c("Communities", "Treatment")
m2<- as.data.frame(list(paste("community",11:20,sep=""), paste("T2")))
colnames(m2)<- c("Communities", "Treatment")
metadata<-rbind(m1,m2)

# 1- Calculate the Shannon diversity index for all samples using the vegan package

raremax<-min(rowSums(community_matrix))
rarefied_data<- rrarefy(community_matrix, raremax)
H <- vegan::diversity(rarefied_data, index = "shannon")

# Using the Shannon diversity measurements obtained in step1, make a graph with a boxplot for each treatment - customize the plot as you wish```

Upvotes: 0

Views: 71

Answers (1)

MrFlick
MrFlick

Reputation: 206232

One way to do this is to join/merge the data. The only trick here is that H is a named vector rather than a data frame. But if we use a bit of dplyr to fo the merge, we can also use tibble to turn it into a data frame. This should work

tibble::enframe(H, name="Communities", value="H") |> 
  left_join(metadata) |> 
  ggplot() + 
    aes(Treatment, H) + 
    geom_boxplot()

boxplot

Upvotes: 2

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