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.

### See Also

See AbundanceCurve for the input object and estimateAbundance for generating the input abundance distribution. Plotting is performed with ggplot.

### Examples

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

[Package alakazam version 0.3.0 Index]