Baxter Dataset

This repository holds the Baxter dataset used in the minimalR tutorials.

baxter.subsample.shared

mothur "#sub.sample(shared=baxter.shared)"
mv baxter.0.03.subsample.shared baxter.subsample.shared

baxter.braycurtis.dist

mothur "#dist.shared(shared=baxter.shared, calc=braycurtis, output=square)"
mv baxter.braycurtis.0.03.square.dist baxter.braycurtis.dist

baxter.groups.ave-std.summary

mothur "#summary.single(shared=baxter.shared, calc=nseqs-sobs-shannon-invsimpson-coverage, subsample=TRUE)"

baxter.braycurtis.pcoa.axes / baxter.braycurtis.pcoa.loadings

mothur "#pcoa(phylip=baxter.braycurtis.dist)"

baxter.braycurtis.nmds_2d.axes / baxter.braycurtis.nmds_2d.stress

mothur "#nmds(phylip=baxter.braycurtis.dist, maxdim=2)"
rm baxter.braycurtis.nmds.iters
mv baxter.braycurtis.nmds.axes baxter.braycurtis.nmds_2d.axes
mv baxter.braycurtis.nmds.stress baxter.braycurtis.nmds_2d.stress

baxter.braycurtis.nmds_3d.axes / baxter.braycurtis.nmds_3d.stress

mothur "#nmds(phylip=baxter.braycurtis.dist, mindim=3)"
rm baxter.braycurtis.nmds.iters
mv baxter.braycurtis.nmds.axes baxter.braycurtis.nmds_3d.axes
mv baxter.braycurtis.nmds.stress baxter.braycurtis.nmds_3d.stress

baxter.rarefaction

mothur "#rarefaction.single(shared=baxter.shared)"
mv baxter.groups.rarefaction baxter.rarefaction

Schubert Dataset

Get raw data files

wget -N https://github.com/SchlossLab/Schubert_clinical_mBio_2014/raw/master/data/process/schubert.metadata.xlsx
wget -N https://github.com/SchlossLab/Schubert_clinical_mBio_2014/raw/master/data/process/schubert.shared.gz
wget -N https://github.com/SchlossLab/Schubert_clinical_mBio_2014/raw/master/data/process/schubert.cons.taxonomy.gz

gunzip schubert.shared.gz schubert.cons.taxonomy.gz

Not everything in the metadata is in the shared file. Need to join on the dataframes

library(tidyverse)
library(readxl)

md <- read_xlsx("schubert.metadata.xlsx") %>% select(sample_id)

read_tsv("schubert.shared") %>%
  inner_join(., md, by=c("Group" = "sample_id")) %>%
  write_tsv("schubert.shared")

schubert.subsample.shared

mothur "#sub.sample(shared=schubert.shared)"
mv schubert.0.03.subsample.shared schubert.subsample.shared

schubert.braycurtis.dist

mothur "#dist.shared(shared=schubert.shared, calc=braycurtis, output=square)"
mv schubert.braycurtis.0.03.square.dist schubert.braycurtis.dist

schubert.groups.ave-std.summary

mothur "#summary.single(shared=schubert.shared, calc=nseqs-sobs-shannon-invsimpson-coverage, subsample=TRUE)"

schubert.braycurtis.pcoa.axes / schubert.braycurtis.pcoa.loadings

mothur "#pcoa(phylip=schubert.braycurtis.dist)"

schubert.braycurtis.nmds_2d.axes / schubert.braycurtis.nmds_2d.stress

mothur "#nmds(phylip=schubert.braycurtis.dist, maxdim=2)"
rm schubert.braycurtis.nmds.iters
mv schubert.braycurtis.nmds.axes schubert.braycurtis.nmds_2d.axes
mv schubert.braycurtis.nmds.stress schubert.braycurtis.nmds_2d.stress

schubert.braycurtis.nmds_3d.axes / schubert.braycurtis.nmds_3d.stress

mothur "#nmds(phylip=schubert.braycurtis.dist, mindim=3)"
rm schubert.braycurtis.nmds.iters
mv schubert.braycurtis.nmds.axes schubert.braycurtis.nmds_3d.axes
mv schubert.braycurtis.nmds.stress schubert.braycurtis.nmds_3d.stress

schubert.rarefaction

mothur "#rarefaction.single(shared=schubert.shared)"
mv schubert.groups.rarefaction schubert.rarefaction