R: Plot the results of alphaDiversity

plotDiversityCurve {alakazam} | R Documentation

## Plot the results of alphaDiversity

### Description

`plotDiversityCurve` plots a `DiversityCurve` object.

### Usage

    plotDiversityCurve(data, colors = NULL, main_title = "Diversity",
      legend_title = "Group", log_x = FALSE, log_y = FALSE,
      xlim = NULL, ylim = NULL, annotate = c("none", "depth"),
      score = c("diversity", "evenness"), silent = FALSE, ...)

### Arguments

`data` | DiversityCurve object returned by alphaDiversity.
`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_x` | if `TRUE` then plot q on a log scale; if `FALSE` plot on a linear scale.
`log_y` | if `TRUE` then plot the diversity/evenness scores on a log scale; if `FALSE` plot on a linear scale.
`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.
`score` | one of `"diversity"` or `"evenness"` specifying which score to plot on the y-asis.
`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 and alphaDiversity for generating DiversityCurve objects for input. Plotting is performed with ggplot.

### Examples

    # Calculate diversity
    div <- alphaDiversity(ExampleDb, group="SAMPLE", nboot=100)

    # Plot diversity
    plotDiversityCurve(div, legend_title="Sample")

    #' # Plot diversity
    plotDiversityCurve(div, legend_title="Sample", score="evenness")

[Package alakazam version 0.3.0 Index]