Associate Microbial Prevalence, Specificity, and Abundance with Gene Presence

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Documentation for package ‘phylogenize’ version 2.0.0.0001

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add.below.LOD Add in taxa that were not observed, assuming this means they were zero-prevalence.
add.sig.descs Add gene descriptions to significant results; return in a tibble.
adjust.db Clean up imported database.
alt.multi.enrich An alternative way to get the enrichment table, using a tbl of results instead of separate inputs for significant results, effect signs, etc.
calc.alpha.power Calculate the FPR and (1 - FNR) for results of a set of tests.
calc.ess Main function to calculate environmental specificity scores.
check.process.metadata Check and process metadata
clean.pheno Remove taxa from a phenotype that aren't in our trees and gene matrices (usually only necessary for testing).
do.clust.plot Make a hybrid tree-heatmap plot showing the taxon distribution of significant hits.
do.fisher Wrapper around 'fisher.test' that starts with string vectors instead of a contingency table.
gene.annot Annotate genes using a gene-to-function table.
get.pheno.plotting.scales Get phenotype plotting scales.
get.top.N Return the significant hits with the N smallest p-values.
get.vsearch.results Read in results from vsearch.
gg.cont.tree Plot continuous trait on a tree.
harmonize.abd.meta Check metadata and abundance matrix against one another
import.pz.db Import the data necessary for *phylogenize* analysis.
install_data Copy and/or unzip downloaded data into the Phylogenize2 database directory.
kable.recolor Function to obtain HTML colors for a particular value.
keep.tips Keep some tips on a tree.
lm.fx.pv Wrapper around _lm_ that returns just the effect size and p-value.
logistic Calculate inverse-logit of a value or vector of values.
logit Calculate logit of a value or vector of values.
make.pos.sig Get vectors of significant genes with positive effect sizes.
make.results.matrix Convert results into a long (vs. wide) format.
make.signs Get effect sizes of genes from result tables.
make.sigs Get vectors of significant genes from result tables.
matrix.plm Perform phylogenetic (or linear) modeling for a single taxon.
multi.enrich Given lists of significant genes (at different thresholds), effect sizes, and gene set mappings, assemble a tbl of results.
non.interactive.plot A fall-back plotting option for when 'hack.tree.labels' fails, designed to produce the same kind of output.
nonequiv.pos.sig Get vectors of significant genes with positive (or negative) effect sizes.
nonparallel.results.generator Fit phylogenetic (or linear) models (single core version, single taxon).
output.enr.table Make a pretty enrichment table.
phylolm.fx.pv Wrapper around _phylolm_ that returns just the effect size and p-value.
plot.labeled.phenotype.trees Edit a list of plotted trees to add fancy highlight labels.
plot.pheno.distributions Plot distributions of a phenotype across taxa.
plot.phenotype.trees Plot a phenotype along a list of trees.
prepare.vsearch.input Prepare input file for alignment
prev.addw Main function to calculate taxon prevalences with additive smoothing.
process.16s Map denoised 16S sequence variants to MIDAS IDs using vsearch.
pv1 Fix p-values that are above 1.
pz.error Throw an error and optionally log it in errmsg.txt.
pz.message Report a message and optionally log it in errmsg.txt.
pz.options Set and get options for phylogenize.
pz.warning Report a warning and optionally log it in errmsg.txt.
read.abd.metadata Read in abundance and metadata file(s).
remove.allzero.abundances Remove rows and columns of a matrix that are all zero.
result.wrapper.plm Fit phylogenetic (or linear) models, or perform POMS.
results.report Create a summary table giving how many tests were significant.
retain.observed.taxa Modify trees to retain only observed taxa (for use with specificity only).
run.vsearch Run vsearch analysis on a FASTA file of sequences.
sanity.check.abundance Sanity-check abundance data
sanity.check.metadata Check that dataset, environment, and sample columns all present
set_data_internal Set data directory to internal
single.cluster.plot Make a hybrid tree-heatmap plot showing the taxon distribution of significant hits.
sum.nonunique.vsearch Sum non-unique rows after vsearch mapping.
tax.annot Annotate taxa using a taxonomy table.
tbl.result.qvs Get q-values for results in tbl format.
threshold.pos.sigs Filter out genes that are almost always present or absent.