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,
...
)

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.

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)


[1] NA



# Plot
plotDensityThreshold(output)

Warning:Removed 1 rows containing missing values (geom_vline()).5

See also

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