plotgg_rankabun: Make rank abundance plot

In surh/AMOR: Abundance Matrix Operations in R

Make rank abundance plot

Description

Make a rank abundance plot from a Dataset object.

Usage

plotgg_rankabun(...)

## Default S3 method:
plotgg_rankabun(
  Tab,
  Map = NULL,
  groupby = NULL,
  sortby = NULL,
  theme = theme_blackbox(),
  variable.name = "Taxon",
  value.name = "Abundance",
  FUN = mean
)

## S3 method for class 'Dataset'
plotgg_rankabun(
  Dat,
  groupby = NULL,
  sortby = NULL,
  theme = theme_blackbox(),
  variable.name = "Taxon",
  value.name = "Abundance",
  FUN = mean
)

Arguments

Tab	A matrix object with samples as columns and taxa as rows.
Map	A data frame with metadata for Tab. Each row must be a sample with row names matching column names in Tab and in the same order as in Tab.
groupby	Variable name to be used for grouping samples before plotting th rank abundance.
sortby	Variable value to be used as reference for sorting the taxa in the rank abundance plot.
theme	ggplot2 theme to be used for plotting.
variable.name	x-axis label in the plot.
value.name	y-axis label in the plot.
FUN	Function to use to aggregate samples according to groupby
Dat	A Dataset object.

Value

A ggplot2 plot.

Author(s)

Sur Herrera Paredes

See Also

plotgg_rankabun2

Examples

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

plotgg_rankabun(Tab = Dat$Tab)
plotgg_rankabun(Tab = Dat$Tab, Map = Dat$Map,groupby = "fraction",sortby = "Soil")

plotgg_rankabun(Dat)
plotgg_rankabun(Dat, groupby = "fraction", sortby = "E")

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