setwd('/Users/BioInfo/Desktop/Supplementary_data_2/')
######### Install and load necessary packages #####
#install.packages('ggplot2')
library('ggplot2')
#install.packages('ellipse')
library('ellipse')
#install.packages('RColorBrewer')
library('RColorBrewer')
#install.packages('dplyr')
library('dplyr')
#install.packages('readr')
library('readr')
#install.packages('tidyr')
library('tidyr')
#install.packages('cowplot')
library('cowplot')
#install.packages('Hmisc')
library('Hmisc')
#install.packages('lavaan')
library('lavaan')
#install.packages('plyr')
library('plyr')
#install.packages('reshape2')
library('reshape2')
#install.packages('ggpubr')
library('ggpubr')
#install.packages('iNEXT')
library('iNEXT')
#install.packages('plotly')
library('plotly')
#install.packages('networkD3')
library('networkD3')
#install.packages('corrplot')
library('corrplot')
#install.packages("PerformanceAnalytics")
library("PerformanceAnalytics")
#install.packages('summarytools')
library('summarytools')
#install.packages('treeio')
library('treeio')
#install.packages('ggtree')
library("ggtree")
#install.packages('phangorn')
library('phangorn')
#install.packages('gridExtra')
library('gridExtra')
#install.packages('grid')
library('grid')
#install.packages('phytools')
library('phytools')
#install.packages('stringr')
library("stringr")
#install.packages('cluster')
library("cluster")
#install.packages('seqinr')
library('seqinr')
#install.packages("wesanderson")
library('wesanderson')
#install.packages('yarrr')
library('yarrr')
#devtools::install_github('mikabr/ggpirate', force = T)
library('ggpirate')
#install.packages('tidyverse')
library('tidyverse')
#install.packages("dabestr")
library("dabestr")
#install.packages("vegan")
library("vegan")
#install.packages("phyloseq")
library('phyloseq')
read.csv('fig_1/study_location_table_5387.csv', header = T, stringsAsFactors = F) -> contigs_per_sra_5387_table
View(contigs_per_sra_5387_table)
View(contigs_per_sra_5387_table)
kruskal.test(Freq ~ Location, data = contigs_per_sra_5387_table)
read.csv('fig_1/study_location_table_5387.csv', header = T, stringsAsFactors = T) -> contigs_per_sra_5387_table
kruskal.test(Freq ~ Location, data = contigs_per_sra_5387_table)
shapiro.test(contigs_per_sra_5387_table$Freq)
