View source: R/DistToNearest.R
plotDensityThreshold | R Documentation |
plotDensityThreshold
plots the results from "density"
method of
findThreshold, including the smoothed density estimate, input nearest neighbor
distance histogram, and threshold selected.
plotDensityThreshold(
data,
cross = NULL,
xmin = NULL,
xmax = NULL,
breaks = NULL,
binwidth = NULL,
title = NULL,
size = 1,
silent = FALSE,
...
)
data |
DensityThreshold object output by the |
cross |
numeric vector of distances from distToNearest to draw as a
histogram below the |
xmin |
minimum limit for plotting the x-axis. If |
xmax |
maximum limit for plotting the x-axis. If |
breaks |
number of breaks to show on the x-axis. If |
binwidth |
binwidth for the histogram. If |
title |
string defining the plot title. |
size |
numeric value for the plot line sizes. |
silent |
if |
... |
additional arguments to pass to ggplot2::theme. |
A ggplot object defining the plot.
See DensityThreshold for the the input object definition and findThreshold for generating the input object. See distToNearest calculating nearest neighbor distances.
# 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)
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