plotDensityThreshold: Plot findThreshold results for the density method

In shazam: Immunoglobulin Somatic Hypermutation Analysis

Plot findThreshold results for the density method

Description

plotDensityThreshold plots the results from "density" method of findThreshold, including the smoothed density estimate, input nearest neighbor distance histogram, and threshold selected.

Usage

plotDensityThreshold(
  data,
  cross = NULL,
  xmin = NULL,
  xmax = NULL,
  breaks = NULL,
  binwidth = NULL,
  title = NULL,
  size = 1,
  silent = FALSE,
  ...
)

Arguments

data	DensityThreshold object output by the "density" method of findThreshold.
cross	numeric vector of distances from distToNearest to draw as a histogram below the data histogram for comparison purposes.
xmin	minimum limit for plotting the x-axis. If NULL the limit will be set automatically.
xmax	maximum limit for plotting the x-axis. If NULL the limit will be set automatically.
breaks	number of breaks to show on the x-axis. If NULL the breaks will be set automatically.
binwidth	binwidth for the histogram. If NULL the binwidth will be set automatically to the bandwidth parameter determined by findThreshold.
title	string defining the plot title.
size	numeric value for the plot line sizes.
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 DensityThreshold for the the input object definition and findThreshold for generating the input object. See distToNearest calculating nearest neighbor distances.

Examples

# Subset example data to one sample as a demo
data(ExampleDb, package="alakazam")
db <- subset(ExampleDb, sample_id == "-1h")

# Use nucleotide Hamming distance and normalize by junction length
db <- distToNearest(db, sequenceColumn="junction", vCallColumn="v_call_genotyped",
                    jCallColumn="j_call", model="ham", normalize="len", nproc=1)

# To find the threshold cut, call findThreshold function for "gmm" method.
output <- findThreshold(db$dist_nearest, method="density")
print(output)

# Plot
plotDensityThreshold(output)

shazam documentation built on Oct. 3, 2023, 1:06 a.m.