mothur_PCoA.R

# Mothur PCoA Dirk sequencing

library(ggplot2)
library(dplyr)
library(tidyr)

# replace metadata with new metadata
meta_new <- read.csv('~/Desktop/Work/dirk_sequencing/data/metadata.csv', stringsAsFactors = FALSE) %>%
mutate(., time = as.character(time))

# read in data
d <- read.table('~/Desktop/dirk.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.unique_list.braycurtis.0.03.lt.pcoa.axes', header = TRUE, stringsAsFactors = FALSE) %>%
mutate(group = tolower(group)) %>%
rename(SampleID = group) %>%
merge(., meta_new, by = 'SampleID')

ggplot(d) +
geom_point(aes(axis1*-1, axis2*-1, col = time, shape = treat))