plotAbundanceCurve: Plot a clonal abundance distribution

In alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

Plot a clonal abundance distribution

Description

plotAbundanceCurve plots the results from estimating the complete clonal relative abundance distribution. The distribution is plotted as a log rank abundance distribution.

Usage

plotAbundanceCurve(
  data,
  colors = NULL,
  main_title = "Rank Abundance",
  legend_title = NULL,
  xlim = NULL,
  ylim = NULL,
  annotate = c("none", "depth"),
  silent = FALSE,
  ...
)

Arguments

data	AbundanceCurve object returned by estimateAbundance.
colors	named character vector whose names are values in the group column 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.
xlim	numeric vector of two values specifying the c(lower, upper) x-axis limits. The lower x-axis value must be >=1.
ylim	numeric vector of two values specifying the c(lower, upper) y-axis limits. The limits on the abundance values are expressed as fractions of 1: use c(0,1) to set the lower and upper limits to 0% and 100%.
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 AbundanceCurve for the input object and estimateAbundance for generating the input abundance distribution. Plotting is performed with ggplot.

Examples

# Estimate abundance by sample and plot
abund <- estimateAbundance(ExampleDb, group="sample_id", nboot=100)
plotAbundanceCurve(abund, legend_title="Sample")

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