mostAbundant

mostAbundant

R Documentation

Get the N most abundant rows (or columns) from a numeric table

Description

Return a subset of an input matrix or data frame, containing only the N most abundant rows (or columns), sorted. Alternatively, a custom set of rows can be returned.

Usage

mostAbundant(
  data,
  N = 10,
  items = NULL,
  extra_items = NULL,
  ignore = NULL,
  others = FALSE,
  rescale = FALSE,
  bycol = FALSE
)

Arguments

`data`	numeric matrix or data frame
`N`	integer Number of rows to return (default `10`).
`items`	character vector. Custom row names to return. If provided, it will override `N` and `extra_items` (default `NULL`).
`extra_items`	character vector. Extra row names to return on top of the N most abundant (default `NULL`)
`ignore`	character. Custom row names to drop before abundance calculation.
`others`	logical. If `TRUE`, an extra row will be returned containing the aggregated abundances of the elements not selected with `N` or `items` (default `FALSE`).
`rescale`	logical. Scale result to percentages column-wise (default `FALSE`).
`bycol`	logical. Operate on columns instead of rows (default `FALSE`).

Value

A matrix or data frame (same as input) with the selected rows (or columns).

Examples

data(Hadza)
Hadza.carb = subsetFun(Hadza, "Carbohydrate metabolism")
# Which are the 20 most abundant KEGG functions in the ORFs related to carbohydrate metabolism?
topCarb = mostAbundant(Hadza.carb$functions$KEGG$tpm, N=20)
# Now print them with nice names.
rownames(topCarb) = paste(rownames(topCarb),
                          Hadza.carb$misc$KEGG_names[rownames(topCarb)], sep="; ")
topCarb
# We can pass this to any R function.
heatmap(topCarb)
# But for convenience we provide wrappers for plotting ggplot2 heatmaps and barplots.
plotHeatmap(topCarb, label_y="TPM")
plotBars(topCarb, label_y="TPM")