taxa_sums: Get summary taxa abundances.

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

Get summary taxa abundances.

Description

Get summary taxa abundances.

Usage

taxa_sums(
  biom,
  rank = -1,
  sort = NULL,
  lineage = FALSE,
  unc = "singly",
  transform = "none"
)

taxa_means(
  biom,
  rank = -1,
  sort = NULL,
  lineage = FALSE,
  unc = "singly",
  transform = "none"
)

taxa_apply(
  biom,
  FUN,
  rank = -1,
  sort = NULL,
  lineage = FALSE,
  unc = "singly",
  transform = "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.
sort	Sort the result. Options: NULL, "asc", or "desc", where NULL will not sort the result. "asc" will sort in ascending order (smallest to largest), and "desc" in descending order (largest to smallest). Ignored when the result is not a simple numeric vector. Default: NULL
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
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. Abbreviations are allowed. Default: "singly"
transform	Transformation to apply. Options are: c("none", "rank", "log", "log1p", "sqrt", "percent"). "rank" is useful for correcting for non-normally distributions before applying regression statistics. Default: "none"
FUN	The function to apply to each row of the taxa_matrix().
...	Optional arguments to FUN.

Value

For taxa_sums and taxa_means, a named numeric vector. For taxa_apply, a named vector or list with the results of FUN. The names are the taxa IDs.

See Also

Other taxa_abundance: sample_sums(), taxa_boxplot(), taxa_clusters(), taxa_corrplot(), taxa_heatmap(), taxa_stacked(), taxa_stats(), taxa_table()

Examples

    library(rbiom) 
    
    taxa_sums(hmp50) %>% head(4)
    
    taxa_means(hmp50, 'Family') %>% head(5)
    
    taxa_apply(hmp50, max) %>% head(5)
    
    taxa_apply(hmp50, fivenum) %>% head(5)

rbiom documentation built on April 3, 2025, 6:39 p.m.