alakazam (version 0.2.2)

plotAbundance: Plots a clonal abundance distribution

Description

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

Usage

plotAbundance(data, colors = NULL, main_title = "Rank Abundance",
  legend_title = NULL, xlim = NULL, ylim = NULL, silent = FALSE, ...)

Arguments

data

data.frame 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.

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 estimateAbundance for generating the input abundance distribution. Plotting is performed with ggplot.

Examples

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

# Plot
abund <- estimateAbundance(df, "SAMPLE", nboot=100)
plotAbundance(abund)