phylogram: Phylogram

In surh/AMOR: Abundance Matrix Operations in R

Phylogram

Description

Make a relative abundance barplot of taxon abundances.

Usage

phylogram(...)

## Default S3 method:
phylogram(
  Tab,
  Map = NULL,
  facet = NULL,
  colname = "Sample",
  variable.name = "Taxon",
  value.name = "Abundance",
  scales = "free_x",
  space = "free_x",
  nrow.legend = 20,
  ntaxa = NULL,
  other_name = "other"
)

## S3 method for class 'Dataset'
phylogram(
  Dat,
  facet = NULL,
  colname = "Sample",
  variable.name = "Taxon",
  value.name = "Abundance",
  scales = "free_x",
  space = "free_x",
  nrow.legend = 20,
  ntaxa = NULL,
  other_name = "other"
)

Arguments

Tab	A matrix object representing samples as columns and taxa as rows.
Map	A data frame with metadata for Tab. One row per sample, and the rows must be named to match the column names in Tab, and they must be in the same order.
facet	facet formula for facet_grid.
colname	Label to be used in the x-axis of the phylogram.
variable.name	Label to be used in for the colors in the phylogram
value.name	Label for the y-axis of the phylogram.
scales	scales option for facet_grid.
space	space option for facet_grid
nrow.legend	number of rows to use in the legend.
ntaxa	Number of taxa to plot, the rest will be collapsed into one category. Samples will be sorted by abundance and the top ntaxa will be plotted.
other_name	Name to give to the collapsed taxa when ntaxa is used.
Dat	A Dataset object.

Value

A ggplot2 object of the plot.

Author(s)

Sur Herrera Paredes

Examples

data(Rhizo)
data(Rhizo.map)
data(Rhizo.tax)
Dat <- create_dataset(Rhizo,Rhizo.map,Rhizo.tax)

Dat.phyl <- collapse_by_taxonomy(Dat = Dat, level = 4)
phylogram(Tab = Dat.phyl$Tab,
          Map = Dat.phyl$Map,
          facet = ~ fraction)
phylogram(Dat.phyl, facet = ~ fraction)
phylogram(Dat.phyl, facet = ~ fraction,
          ntaxa = 5)

surh/AMOR documentation built on Feb. 21, 2023, 6:31 a.m.