R: Plot the results of diversity testing

plotDiversityTest {alakazam} | R Documentation

## Plot the results of diversity testing

### Description

`plotDiversityTest` plots summary data for a `DiversityCurve` object with mean and a line range indicating plus/minus one standard deviation.

### Usage

    plotDiversityTest(data, q, colors = NULL, main_title = "Diversity",
      legend_title = "Group", log_d = FALSE, annotate = c("none",
      "depth"), silent = FALSE, ...)

### Arguments

`data` | DiversityCurve object returned by alphaDiversity.
`q` | diversity order to plot the test for.
`colors` | named character vector whose names are values in the `group` column of the `data` slot 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.
`log_d` | if `TRUE` then plot the diversity scores D on a log scale; if `FALSE` plot on a linear scale.
`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 alphaDiversity for generating input. Plotting is performed with ggplot.

### Examples

    # Calculate diversity
    div <- alphaDiversity(ExampleDb, group="SAMPLE", min_q=0, max_q=2, step_q=1, nboot=100)

    # Plot results at q=0 (equivalent to species richness)
    plotDiversityTest(div, 0, legend_title="Sample")

    # Plot results at q=2 (equivalent to Simpson's index)
    plotDiversityTest(div, q=2, legend_title="Sample")

[Package alakazam version 0.3.0 Index]