R: Plots a clonal abundance distribution

plotAbundanceCurve {alakazam}

R Documentation

Plots a clonal abundance distribution

Description

plotAbundanceCurve plots the results from estimating the complete clonal relative abundance distribution. The distribution is plotted as a log rank abundance distribution.

Usage

plotAbundanceCurve(data, colors = NULL, main_title = "Rank Abundance",
  legend_title = NULL, xlim = NULL, ylim = NULL,
  annotate = c("none", "depth"), silent = FALSE, ...)

Arguments

`data`	AbundanceCurve object returned by estimateAbundance.
`colors`	named character vector whose names are values in the `group` column of `data` and whose values are colors to assign to those group names.
`main_title`	string specifying the plot title.
`legend_title`	string specifying the legend title.
`xlim`	numeric vector of two values specifying the `c(lower, upper)` x-axis limits.
`ylim`	numeric vector of two values specifying the `c(lower, upper)` y-axis limits.
`annotate`	string defining whether to added values to the group labels of the legend. When `"none"` (default) is specified no annotations are added. Specifying (`"depth"`) adds sequence counts to the labels.
`silent`	if `TRUE` do not draw the plot and just return the ggplot2 object; if `FALSE` draw the plot.
`...`	additional arguments to pass to ggplot2::theme.

Value

A ggplot object defining the plot.

Examples

# Estimate abundance by sample and plot
abund <- estimateAbundance(ExampleDb, group="SAMPLE", nboot=100)
plotAbundanceCurve(abund, legend_title="Sample")