tcR (version 1.1)

vis.V.usage: Histogram of segments usage.

Description

Plot a histogram or a grid of histograms of V- / J-usage.

Usage

vis.V.usage(.data, .cast.freq = T, .main = "V-usage", .ncol = 3,
  .coord.flip = F, .dodge = F, ...)

Arguments

.data

Mitcr data frame or a list with mitcr data frames.

.cast.freq

If T than cast freq.Vb (for vis.V.usage) or freq.Jb (for vis.J.usage) on .data before plotting.

.main

Main title of the plot.

.ncol

Number of columns in a grid of histograms if .data is a list and .dodge is F.

.coord.flip

If T than flip coordinates.

.dodge

If .data is a list, than if this is T plot V-usage for all data frames to the one histogram.

...

Parameter passed to freq.segments. By default the function compute V-usage or J-usage for beta chains w/o using read counts and w/ "Other" segments.

Value

• ggplot object.

Examples

# Load your data.
load('immdata.rda')
# Compute V-usage statistics.
imm1.vs <- freq.Vb(immdata[[1]])
# Two eqivalent calls for plotting the V-usage for all data frames on the one plot:
vis.V.usage(immdata, .cast.freq = T, .main = 'Immdata V-usage [1]', .dodge = T)
vis.V.usage(imm1.vs, .cast.freq = F, .main = 'Immdata V-usage [2]', .dodge = T)
# Plot a grid of histograms - one histogram for V-usage for each data frame in .data.
vis.V.usage(immdata, .cast.freq = T, .main = 'Immdata V-usage [3]', .dodge = F, .other = F)