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Summarize community data by species, genus, family, etc.

Source: R/aggregate.R
aggregate.Rd

ncopiesperml is summed for in each sample. Species whose names contain "unidentified" are removed by default.

Usage

summarize_ncopies(community_df, .by = .data$species, rm_unidentified = TRUE)

pivot_wider_ncopies(community_df, .by = .data$species, rm_unidentified = TRUE)

distinct_taxonomy(community_df, rm_unidentified = TRUE)

Arguments

community_df

A community data frame, e.g., output of ranemone::read_tsv_xz("community_qc3nn_target.tsv.xz").

.by

Columns by which to summarize, e.g., species, genus, and/or family.

rm_unidentified

A logical value indicating whether to remove "unidentified" species.

Value

summarize_ncopies() returns a data frame in longer format.

pivot_wider_ncopies() returns a community composition matrix in wider format (samples x species).

Examples

if (FALSE) { # \dontrun{
community_df = ranemone::read_tsv_xz("community_qc3nn_target.tsv.xz")
species_df = ranemone::summarize_ncopies(community_df, .by = species)
genus_df = ranemone::summarize_ncopies(community_df, .by = genus, rm_unidentified = FALSE)

species_mat = ranemone::pivot_wider_ncopies(community_df, .by = species)
family_mat = ranemone::pivot_wider_ncopies(community_df, .by = family, rm_unidentified = FALSE)

taxonomy = ranemone::distinct_taxonomy(community_df)
} # }