R: Integrated Analysis and Visualization of Microbiome Data

# Integrated Analysis and Visualization of Microbiome Data

## Documentation for package ‘rbiom’ version 3.1.0

- DESCRIPTION file
- Package README

## Help Pages

A B C D E G H M N P R S T W misc

## -- A --

adiv_boxplot | Visualize alpha diversity with boxplots.
adiv_corrplot | Visualize alpha diversity with scatterplots and trendlines.
adiv_matrix | Calculate the alpha diversity of each sample.
adiv_stats | Test alpha diversity for associations with metadata.
adiv_table | Calculate the alpha diversity of each sample.
adiv_vector | Calculate the alpha diversity of each sample.
as.list.rbiom | Convert an rbiom object to a base R list.
as.matrix.rbiom | Convert an rbiom object to a simple count matrix.
as_rbiom | Convert a variety of data types to an rbiom object.

## -- B --

babies | Longitudinal Stool Samples from Infants (n = 2,684)
bdiv_boxplot | Visualize BIOM data with boxplots.
bdiv_clusters | Cluster samples by beta diversity k-means.
bdiv_corrplot | Visualize beta diversity with scatterplots and trendlines.
bdiv_distmat | Distance / dissimilarity between samples.
bdiv_heatmap | Display beta diversities in an all vs all grid.
bdiv_matrix | Distance / dissimilarity between samples.
bdiv_ord_plot | Ordinate samples and taxa on a 2D plane based on beta diversity distances.
bdiv_ord_table | Calculate PCoA and other ordinations, including taxa biplots and statistics.
bdiv_stats | Test beta diversity for associations with metadata.
bdiv_table | Distance / dissimilarity between samples.
bdply | Apply a function to each subset of an rbiom object.
biom_inflate | Inflate Relative Abundances to Integer Counts
biom_merge | Combine several rbiom objects into one.
biom_relativize | Relativize Counts to Proportions
biom_rescale | Rescale Counts to a Specific Range
blply | Apply a function to each subset of an rbiom object.

## -- C --

convert_to | Convert biom data to an external package class
convert_to_animalcules | Convert biom data to an external package class
convert_to_biomformat | Convert biom data to an external package class
convert_to_phyloseq | Convert biom data to an external package class
convert_to_SE | Convert biom data to an external package class
convert_to_TSE | Convert biom data to an external package class

## -- D --

distmat_ord_table | Run ordinations on a distance matrix.
distmat_stats | Run statistics on a distance matrix vs a categorical or numeric variable.

## -- E --

export | Export data to QIIME 2 or mothur.

## -- G --

gems | Global Enteric Multicenter Study (n = 1,006)
glimpse.rbiom | Get a glimpse of your metadata.

## -- H --

hmp50 | Human Microbiome Project - demo dataset (n = 50)

## -- M --

matrix_ops | Deprecated matrix transformations
modify_metadata | Create, modify, and delete metadata fields.
mtx_percent | Deprecated matrix transformations
mtx_rarefy | Deprecated matrix transformations
mtx_rescale | Deprecated matrix transformations
mutate.rbiom | Create, modify, and delete metadata fields.

## -- N --

na.omit.rbiom | Subset an rbiom object by sample names, OTU names, metadata, or taxonomy.

## -- P --

plot_heatmap | Create a heatmap with tracks and dendrograms from any matrix.
pull.rbiom | Map sample names to metadata field values.

## -- R --

rarefy | Rarefy Counts to a Constant Depth
rarefy_cols | Deprecated matrix transformations
rare_corrplot | Visualize rarefaction curves with scatterplots and trendlines.
rare_multiplot | Combines rare_corrplot and rare_stacked into a single figure.
rare_stacked | Visualize the number of observations per sample.
read_biom | Parse counts, metadata, taxonomy, and phylogeny from a BIOM file.
read_fasta | Parse a fasta file into a named character vector.
read_tree | Read a newick formatted phylogenetic tree.
rename.rbiom | Create, modify, and delete metadata fields.
rescale_cols | Deprecated matrix transformations
rescale_rows | Deprecated matrix transformations

## -- S --

sample_apply | Summarize the taxa observations in each sample.
sample_sums | Summarize the taxa observations in each sample.
slice.rbiom | Subset to a specific number of samples.
slice_head.rbiom | Subset to a specific number of samples.
slice_max.rbiom | Subset to a specific number of samples.
slice_metadata | Subset to a specific number of samples.
slice_min.rbiom | Subset to a specific number of samples.
slice_sample.rbiom | Subset to a specific number of samples.
slice_tail.rbiom | Subset to a specific number of samples.
stats_boxplot | Visualize categorical metadata effects on numeric values.
stats_corrplot | Visualize regression with scatterplots and trendlines.
stats_table | Run non-parametric statistics on a data.frame.
subset | Subset an rbiom object by sample names, OTU names, metadata, or taxonomy.
subset.rbiom | Subset an rbiom object by sample names, OTU names, metadata, or taxonomy.
subset_taxa | Subset an rbiom object by sample names, OTU names, metadata, or taxonomy.
suggest_inflate_depths | Suggest Inflation Depths
suggest_rarefy_depth | Suggest Rarefaction Depth

## -- T --

taxa_apply | Get summary taxa abundances.
taxa_boxplot | Visualize BIOM data with boxplots.
taxa_clusters | Cluster samples by taxa abundances k-means.
taxa_corrplot | Visualize taxa abundance with scatterplots and trendlines.
taxa_heatmap | Display taxa abundances as a heatmap.
taxa_map | Map OTUs names to taxa names at a given rank.
taxa_matrix | Taxa abundances per sample.
taxa_means | Get summary taxa abundances.
taxa_stacked | Display taxa abundances as a stacked bar graph.
taxa_stats | Test taxa abundances for associations with metadata.
taxa_sums | Get summary taxa abundances.
taxa_table | Taxa abundances per sample.
tree_subset | Create a subtree by specifying tips to keep.

## -- W --

with | Evaluate expressions on metadata.
with.rbiom | Evaluate expressions on metadata.
within.rbiom | Evaluate expressions on metadata.
write_biom | Save an rbiom object to a file.
write_counts | Save an rbiom object to a file.
write_fasta | Save an rbiom object to a file.
write_metadata | Save an rbiom object to a file.
write_mothur | Export data to QIIME 2 or mothur.
write_qiime2 | Export data to QIIME 2 or mothur.
write_taxonomy | Save an rbiom object to a file.
write_tree | Save an rbiom object to a file.
write_xlsx | Save an rbiom object to a file.

## -- misc --

[.rbiom | Subset an rbiom object by sample names, OTU names, metadata, or taxonomy.