vis.shared.clonotypes: Visualisation of shared clonotypes occurrences among...

In imminfo/tcr: Advanced Data Analysis of Immune Receptor Repertoires

Description

Visualise counts or proportions of shared clonotypes among repertoires. Code adapted from https://www.r-bloggers.com/ggplot2-cheatsheet-for-visualizing-distributions/.

Usage

vis.shared.clonotypes(
  .shared.rep,
  .x.rep = NA,
  .y.rep = NA,
  .title = NA,
  .ncol = 3,
  .point.size.modif = 1,
  .cut.axes = T,
  .density = T,
  .lm = T,
  .radj.size = 3.5,
  .plot = T
)

Arguments

.shared.rep	Shared repertoires, as from shared.repertoire function.
.x.rep	Which repertoire show on x-axis. Either a name or an index of a repertoire in the .shared.rep or NA to choose all repertoires.
.y.rep	Which repertoire show on y-axis. Either a name or an index of a repertoire in the .shared.rep or NA to choose all repertoires.
.title	Main title of the plot.
.ncol	Number of columns in the resulting plot.
.point.size.modif	Modify this to correct sizes of points.
.cut.axes	If T than cut axes' limits to show only frequencies that exists.
.density	If T than plot densities of shared and unique clonotypes.
.lm	If T than fit and plot a linear model to shared clonotypes.
.radj.size	Size of the text for R^2-adjusted.
.plot	If F than return grobs instead of plotting.

Value

ggplot2 object or plot

See Also

shared.repertoire

Examples

## Not run: 
data(twb)
# Show shared nucleotide clonotypes of all possible pairs
# using the Read.proportion column
twb.sh <- shared.repertoire(twb, "n0rp")
vis.shared.clonotypes(twb.sh, .ncol = 4)

# Show shared amino acid + Vseg clonotypes of pairs
# including the Subj.A (the first one) using
# the Read.count column.
twb.sh <- shared.repertoire(twb, "avrc")
vis.shared.clonotypes(twb.sh, 1, NA, .ncol = 4)
# same, just another order of axis
vis.shared.clonotypes(twb.sh, NA, 1, .ncol = 4)

# Show shared nucleotide clonotypes of Subj.A (the first one)
# Subj.B (the second one) using the Read.proportion column.
twb.sh <- shared.repertoire(twb, "n0rp")
vis.shared.clonotypes(twb.sh, 1, 2)

# Show the same plot, but with much larget points.
vis.shared.clonotypes(twb.sh, 1, 2, .point.size.modif = 3)

## End(Not run)

imminfo/tcr documentation built on June 13, 2020, 7:01 a.m.