shazam (version 1.2.0)

plotDensityThreshold: 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,
  ...
)

Value

A ggplot object defining the plot.

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.

See Also

See DensityThreshold for the the input object definition and findThreshold for generating the input object. See distToNearest calculating nearest neighbor distances.

Examples

# \donttest{
# 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)
# }