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; ifFALSE
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)
Running defineClonesScoper in bulk mode and only keep heavy chains
# Plot clonal summaries
plot(results, binwidth=0.02)
See also¶
See ScoperClones for the the input object definition.
See spectralClones, identicalClones and hierarchicalClones
for generating the input object.