8. R session¶
In this hands-on we will use R to run analyses and create charts from the abundance tables that we generated with Kraken2.
First of all, in R, we must set up the folder which contains the abundance table:
setwd("~/Documents/WORK/2-PROJECTS/HiddenFoods/HiddenFoods_analysis/krk2_genome_length_normalized_abundances_July2019/species")
Then we can import the abundance table files:
# --> you can edit the files, eg remove last column 'Detail!
# dataframes in R must do not allow identical row names, force row names as numbering by using row.names=NULL.
#EOF issue with single quotes (') in species names, use read.delim
HiddenFoods_Jan2019.krk2.norm.species = read.delim("HiddenFoods_Jan2019.krk2.rcf.abundance.species.norm2.final", header=T, fill=T, row.names=NULL, sep="\t")
HiddenFoods_May2019.krk2.norm.species = read.delim("HiddenFoods_May2019.krk2.rcf.abundance.species.norm2.final", header=T, fill=T, row.names=NULL, sep="\t")
Warinner2014.krk2.norm.species = read.delim("Warinner2014.krk2.rcf.abundance.species.norm2.final", header=T, fill=T, row.names=NULL, sep="\t")
Velsko_modern_calculus.krk2.norm.species = read.delim("Velsko_modern_calculus.krk2.rcf.abundance.species.norm2.final", header=T, fill=T, row.names=NULL, sep="\t")
Velsko_ancient_calculus_total.krk2.norm.species = read.delim("Velsko_ancient_calculus_total.krk2.rcf.abundance.species.norm2.final", header=T, fill=T, row.names=NULL, sep="\t")
Plaque.krk2.norm.species = read.delim("Plaque.krk2.rcf.abundance.species.norm2.final", header=T, fill=T, row.names=NULL, sep="\t")
Mann2018.krk2.norm.species = read.delim("Mann2018.krk2.rcf.abundance.species.norm2.final", header=T, fill=T, row.names=NULL, sep="\t")
Baboons_Ozga.krk2.norm.species = read.delim("Baboons_Ozga.krk2.rcf.abundance.species.norm2.final", header=T, fill=T, row.names=NULL, sep="\t")
Weyrich2017.krk2.norm.species = read.delim("Weyrich2017.krk2.rcf.abundance.species.norm2.final", header=T, fill=T, row.names=NULL, sep="\t")
Baboons_Egypt_all.krk2.norm.species = read.delim("Baboons_Egypt_all.krk2.rcf.abundance.species.flt10.teeth.env.norm2.final", header=T, fill=T, row.names=NULL, sep="\t")
Baboons_Egypt_nofilter.krk2.norm.species = read.delim("Baboons_Egypt_nofilter.krk2.rcf.abundance.species.norm2.final", header=T, fill=T, row.names=NULL, sep="\t")
Baboons_Egypt_teeth.krk2.norm.species = read.delim("Baboons_Egypt_teeth.krk2.rcf.abundance.species.norm2.final", header=T, fill=T, row.names=NULL, sep="\t")
Skin.krk2.norm.species = read.delim("Skin.krk2.rcf.abundance.species.norm2.final", header=T, fill=T, row.names=NULL, sep="\t")
ObregonTito_gut.krk2.norm.species = read.delim("ObregonTito_gut.krk2.rcf.abundance.species.norm2.final", header=T, fill=T, row.names=NULL, sep="\t")
Soil.krk2.norm.species = read.delim("Soil.krk2.rcf.abundance.species.norm2.final", header=T, fill=T, row.names=NULL, sep="\t")
Chimps.krk2.norm.species = read.delim("Chimps_Ozga.krk2.rcf.abundance.species.norm2.final", header=T, fill=T, row.names=NULL, sep="\t")
Brealey_animals.krk2.norm.species = read.delim("Brealey_animals.krk2.rcf.abundance.species.norm2.final", header=T, fill=T, row.names=NULL, sep="\t")
Brealey_animals.krk2.norm.species = Brealey_animals.krk2.norm.species[,-c(2:5,7,8)] #remove Blanks from filtrated Brealey, Gb1reg/flt, Gb2reg/flt
Eisenhofer_Japan_flt.krk2.norm.species = read.table("Eisenhofer_Japan.krk2.rcf.abundance.species.norm2.final.flt", header=T, fill=T, row.names=NULL, sep="\t")
Eisenhofer_Japan_flt.krk2.norm.species = Eisenhofer_Japan_flt.krk2.norm.species[,-c(19,20)] #remove EBC-2 in Eisenhofer which has no classified species, and Details column.