taxa_matrix: Taxa abundances per sample.

In cmmr/rbiom: Read/Write, Analyze, and Visualize 'BIOM' Data

Taxa abundances per sample.

Description

• taxa_matrix() - Accepts a single rank and returns a matrix.

• taxa_table() - Can accept more than one rank and returns a tibble data.frame.

Usage

taxa_table(
  biom,
  rank = -1,
  taxa = 6,
  lineage = FALSE,
  md = ".all",
  unc = "singly",
  other = FALSE,
  trans = "none"
)

taxa_matrix(
  biom,
  rank = -1,
  taxa = NULL,
  lineage = FALSE,
  sparse = FALSE,
  unc = "singly",
  other = FALSE,
  trans = "none"
)

Arguments

biom	An rbiom object, such as from as_rbiom(). Any value accepted by as_rbiom() can also be given here.
rank	What rank(s) of taxa to display. E.g. "Phylum", "Genus", ".otu", etc. An integer vector can also be given, where 1 is the highest rank, 2 is the second highest, -1 is the lowest rank, -2 is the second lowest, and 0 is the OTU "rank". Run biom$ranks to see all options for a given rbiom object. Default: -1.
taxa	Which taxa to display. An integer value will show the top n most abundant taxa. A value 0 <= n < 1 will show any taxa with that mean abundance or greater (e.g. 0.1 implies >= 10%). A character vector of taxa names will show only those named taxa. Default: 6.
lineage	Include all ranks in the name of the taxa. For instance, setting to TRUE will produce ⁠Bacteria; Actinobacteria; Coriobacteriia; Coriobacteriales⁠. Otherwise the taxa name will simply be Coriobacteriales. You want to set this to TRUE when unc = "asis" and you have taxa names (such as Incertae_Sedis) that map to multiple higher level ranks. Default: FALSE
md	Dataset field(s) to include in the output data frame, or '.all' to include all metadata fields. Default: '.all'
unc	How to handle unclassified, uncultured, and similarly ambiguous taxa names. Options are: "singly" - Replaces them with the OTU name. "grouped" - Replaces them with a higher rank's name. "drop" - Excludes them from the result. "asis" - To not check/modify any taxa names. Default: "singly" Abbreviations are allowed.
other	Sum all non-itemized taxa into an "Other" taxa. When FALSE, only returns taxa matched by the taxa argument. Specifying TRUE adds "Other" to the returned set. A string can also be given to imply TRUE, but with that value as the name to use instead of "Other". Default: FALSE
trans	Transformation to apply. Options are: c("none", "rank", "log", "log1p", "sqrt"). "rank" is useful for correcting for non-normally distributions before applying regression statistics. Default: "none"
sparse	If true, returns a sparse matrix as described by slam::simple_triplet_matrix(), otherwise returns a normal R matrix object. Default: FALSE

Value

• taxa_matrix() - A numeric matrix with taxa as rows, and samples as columns.

• taxa_table() - A tibble data frame with column names .sample, .taxa, .abundance, and any requested by md.

See Also

Other taxa_abundance: taxa_boxplot(), taxa_corrplot(), taxa_heatmap(), taxa_stacked(), taxa_stats(), taxa_sums()

Examples

    library(rbiom)
    
    biom$ranks
    
    taxa_matrix(hmp50, 'Phylum')[1:4,1:6]
    
    taxa_table(hmp50, 'Phylum')

cmmr/rbiom documentation built on April 28, 2024, 6:38 a.m.