alakazam (version 1.3.0)

plotAbundanceCurve: 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,
  ...
)

Value

A ggplot object defining the plot.

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.

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")