plotCloneSummary: Plot clonal clustering summary

Description Usage Arguments Value See Also Examples

View source: R/Functions.R

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

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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

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

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

scoper documentation built on Aug. 11, 2020, 1:07 a.m.