plotCloneSummary - 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.

Examples

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

Running defineClonesScoper in bulk mode and only keep heavy chains


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

4

See also

See ScoperClones for the the input object definition.
See spectralClones, identicalClones and hierarchicalClones for generating the input object.