alakazam (version 0.2.11)

plotDiversityTest: Plot the results of TestDiversity

Description

plotDiversityTest plots a DiversityTest object as the mean with a line range indicating plus/minus one standard deviation.

Usage

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

Arguments

data

DiversityTest object returned by testDiversity.

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 testDiversity for generating DiversityTest objects for input. Plotting is performed with ggplot.

Examples

# NOT RUN {
# All groups pass default minimum sampling threshold of 10 sequences
div <- testDiversity(ExampleDb, "SAMPLE", q=0, nboot=100)
plotDiversityTest(div, legend_title="Sample")

# }