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.

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")