tests/testthat/test-prop_tax_down.R

In JCSzamosi/aftersl1p: Generate Summary Graphics and Basic Analysis of 16s Data

# Test prop_tax_down() ---------------------------------------------------------

test_that('prop_tax_down() works without and indic',{
    ## Read in the data

    ### This OTU table is used throughout this test
    otumat = read.csv('prop_tax_down/otumat.csv', row.names = 1)
    ### This sample data (mapfile) is used throughout this test
    samdat = read.csv('prop_tax_down/samdat.csv', row.names = 1)

    ### In this file, every unique value at every taxonomic level has identical
    ### values above that level. I.e. there are no cases where two rows have the
    ### same genus, but different families.
    taxmat = read.csv('prop_tax_down/taxmat_unique.csv', row.names = 1)

    ### This file is what `prop_tax_down()` should do to `taxmat`
    taxmat_propped = read.csv('prop_tax_down/taxmat_unique_propped.csv',
                              row.names = 1)

    ### This file contains some genera that have the same name, but are in
    ### different families.
    taxmat_ambig = read.csv('prop_tax_down/taxmat_ambig.csv', row.names = 1)

    ### This file is what `prop_tax_down()` should do to `taxmat_ambig` if
    ### dbig=TRUE
    taxmat_pr_dbg = read.csv('prop_tax_down/taxmat_ambig_propped_dbig.csv',
                             row.names = 1)

    ### This file is what `prop_tax_down()` should do to `taxmat_ambig` if
    ### dbig=FALSE
    taxmat_pr_ndb = read.csv('prop_tax_down/taxmat_ambig_propped_nodbig.csv',
                             row.names = 1)

    ## Make the unique ps obj
    ps = phyloseq::phyloseq(phyloseq::otu_table(otumat, taxa_are_rows = TRUE),
                  phyloseq::tax_table(as.matrix(taxmat)),
                  phyloseq::sample_data(samdat))

    ## Make the propped ps obj (should match prop_tax_down(ps))
    ps_propped = ps
    phyloseq::tax_table(ps_propped) = phyloseq::tax_table(as.matrix(taxmat_propped))

    ## Make the ambig ps obj
    ps_ambig = ps
    phyloseq::tax_table(ps_ambig) = phyloseq::tax_table(as.matrix(taxmat_ambig))

    # Make the dbigged ps obj
    ps_dbig = ps
    phyloseq::tax_table(ps_dbig) = phyloseq::tax_table(as.matrix(taxmat_pr_dbg))

    ## Make the non-dbigged ps obj
    ps_ndb = ps
    phyloseq::tax_table(ps_ndb) = phyloseq::tax_table(as.matrix(taxmat_pr_ndb))

    expect_equal(prop_tax_down(ps, indic = FALSE),
                 ps_propped) # propagate only (nothing to disambiguate)
    expect_equal(prop_tax_down(ps_propped, indic = FALSE),
                 ps_propped) # do nothing
    expect_equal(prop_tax_down(ps_ambig, indic = FALSE),
                 ps_dbig) # propagate and disambiguate
    expect_equal(prop_tax_down(ps_ambig, indic = FALSE, dbig = FALSE),
                 ps_ndb) # propagate only (fail to disambiguate)
})

# Test dbig_genera() -----------------------------------------------------------

test_that('dbig_genera() works',{
    ## Read in the data

    ### The taxa table with no ambiguous genera
    taxmat = read.csv('dbig_genera/taxmat_unique.csv', row.names = 1)
    ### The taxa table with ambiguous genera
    taxmat_ambig = read.csv('dbig_genera/taxmat_ambig.csv', row.names = 1)
    ### The taxa table with disambiguated genera
    taxmat_dbig = read.csv('dbig_genera/taxmat_dbig.csv', row.names = 1)

    ### The OTU and sample data (map) files
    otumat = read.csv('dbig_genera/otumat.csv', row.names = 1)
    samdat = read.csv('dbig_genera/samdat.csv', row.names = 1)

    ## Make the unique ps obj (should match itself)
    ps = phyloseq::phyloseq(phyloseq::otu_table(otumat, taxa_are_rows = TRUE),
                  phyloseq::tax_table(as.matrix(taxmat)),
                  phyloseq::sample_data(samdat))

    ## Make the ambig ps obj
    ps_ambig = ps
    phyloseq::tax_table(ps_ambig) = phyloseq::tax_table(as.matrix(taxmat_ambig))

    ## Make the disambiguated ps obj (should match ambig)
    ps_dbig = ps
    phyloseq::tax_table(ps_dbig) = phyloseq::tax_table(as.matrix(taxmat_dbig))

    expect_equal(dbig_genera(ps), ps) #nothing to do, output should match input
    expect_equal(dbig_genera(ps_ambig), ps_dbig) #check output
})