Melt Taxa into a Rank-level Long Table — melt

Neutral alias of psmelt_taxa() for taxonomic-rank long table export.

Usage

melt_taxa(
  object,
  taxonomic_rank = c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species"),
  relative = TRUE,
  what = c("sum_intensity", "mean_intensity", "median_intensity"),
  na.rm = TRUE,
  value_name = "abundance"
)

Arguments

object: A microbiome_dataset object.
taxonomic_rank: Taxonomic rank used for aggregation.
relative: Should abundance be expressed as relative abundance?
what: Aggregation method used within each rank.
na.rm: Should missing values be removed before aggregation?
value_name: Name of the abundance column in the output.

Value

A data frame in long format.

Examples

data("global_patterns", package = "microbiomedataset")

x <- melt_taxa(global_patterns, taxonomic_rank = "Genus")
head(x[, c("sample_id", "Genus", "abundance")])
#>   sample_id         Genus    abundance
#> 1    AQC1cm          4-29 0.5340725502
#> 2    AQC1cm      4041AA30 0.0000000000
#> 3    AQC1cm           A17 0.8746237084
#> 4    AQC1cm   Abiotrophia 0.0000000000
#> 5    AQC1cm Acaryochloris 0.0052303079
#> 6    AQC1cm   Acetivibrio 0.0005811453