plotAbundanceCurve - Plots 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.
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.

Examples

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

2

See also

See AbundanceCurve for the input object and estimateAbundance for generating the input abundance distribution. Plotting is performed with ggplot.