plotDiversityCurve: Plot the results of alphaDiversity

In alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

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_id", nboot=100)

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

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

alakazam documentation built on Sept. 30, 2023, 9:07 a.m.