plotCloneSummary: Plot clonal clustering summary

In scoper: Spectral Clustering-Based Method for Identifying B Cell Clones

Plot clonal clustering summary

Description

plotCloneSummary plots the results in a ScoperClones object returned by spectralClones, identicalClones or hierarchicalClones. Includes the minimum inter (between) and maximum intra (within) clonal distances and the calculated efective threshold.

Usage

plotCloneSummary(
  data,
  xmin = NULL,
  xmax = NULL,
  breaks = NULL,
  binwidth = NULL,
  title = NULL,
  size = 0.75,
  silent = FALSE,
  ...
)

Arguments

data	ScoperClones object output by the spectralClones, identicalClones or hierarchicalClones.
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.
title	string defining the plot title.
size	numeric value for lines in the plot.
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 ScoperClones for the the input object definition. See spectralClones, identicalClones and hierarchicalClones for generating the input object.

Examples

# Find clones
results <- hierarchicalClones(ExampleDb, threshold=0.15)

# Plot clonal summaries
plot(results, binwidth=0.02)

scoper documentation built on Oct. 6, 2023, 5:09 p.m.