alakazam (version 0.2.2)

plotDiversityCurve: Plot the results of rarefyDiversity

Description

plotDiversityCurve plots a DiversityCurve object.

Usage

plotDiversityCurve(data, colors = NULL, main_title = "Diversity",
  legend_title = NULL, log_q = TRUE, log_d = TRUE, xlim = NULL,
  ylim = NULL, annotate = c("none", "depth"), silent = FALSE, ...)

Arguments

data

DiversityCurve object returned by rarefyDiversity.

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_q

if TRUE then plot $q$ on a log scale; if FALSE plot on a linear scale.

log_d

if TRUE then plot the diversity scores $D$ 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.

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 rarefyDiversity for generating DiversityCurve objects for input. Plotting is performed with ggplot.

Examples

# Load example data
file <- system.file("extdata", "ExampleDb.gz", package="alakazam")
df <- readChangeoDb(file)

# All groups pass default minimum sampling threshold of 10 sequences
div <- rarefyDiversity(df, "SAMPLE", step_q=0.1, max_q=10, nboot=100)
plotDiversityCurve(div, legend_title="Sample")