In eckartbindewald/bfxapps2: R Bioinformatics Applications

knitr::opts_chunk$set(echo = TRUE)

Preliminaries

remote_dir="https://raw.githubusercontent.com/PacktPublishing/R-Bioinformatics-Cookbook/master"
if (!require(phyloseq)) {
  BiocManager::install("phyloseq")
}
library(phyloseq)

##hdf5
biom_file <- file.path(remote_dir, "datasets", "ch5", "rich_sparse_otu_table.biom")
qiime <- import_biom(biom_file)
str(qiime)
print(qiime@sam_data)

Visualization

#        BarcodeSequence  LinkerPrimerSequence BODY_SITE Description
#Sample1    CGCTTATCGAGA CATGCTGCCTCCCGTAGGAGT       gut   human gut
#Sample2    CATACCAGTAGC CATGCTGCCTCCCGTAGGAGT       gut   human gut
#Sample3    CTCTCTACCTGT CATGCTGCCTCCCGTAGGAGT       gut   human gut
#Sample4    CTCTCGGCCTGT CATGCTGCCTCCCGTAGGAGT      skin  human skin
#Sample5    CTCTCTACCAAT CATGCTGCCTCCCGTAGGAGT      skin  human skin
#Sample6    CTAACTACCAAT CATGCTGCCTCCCGTAGGAGT      skin  human skin

tax_table(qiime)
otu_table(qiime)
sample_data(qiime)

Visualization 2

mothur <- import_mothur(
  mothur_list_file = file.path(remote_dir, "datasets", "ch5", "esophagus.fn.list"),
  mothur_group_file = file.path(remote_dir, "datasets", "ch5", "esophagus.good.groups"),
  mothur_tree_file = file.path(remote_dir, "datasets", "ch5", "esophagus.tree")
)
otu_table(mothur)