Make rank abundance plot

Source: R/plotgg_rankabun.r

Make a rank abundance plot from a Dataset object.

plotgg_rankabun(...)

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

# S3 method for 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.

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")