Public repertoire visualisation

Usage

# S3 method for class 'immunr_public_repertoire'
vis(.data, .plot = c("freq", "clonotypes"), ...)

Arguments

.data

Public repertoire, an output from pubRep.

.plot

A string specifying the plot type:

• "freq" for visualisation of the distribution of occurrences of clonotypes and their frequencies using vis_public_frequencies.

• "clonotypes" for visualisation of public clonotype frequenciy correlations between pairs of samples using vis_public_clonotypes

...

Further arguments passed vis_public_frequencies or vis_public_clonotypes, depending on the ".plot" argument.

Value

A ggplot2 object.

Examples

# \dontrun{
data(immdata)
immdata$data <- lapply(immdata$data, head, 300)
pr <- pubRep(immdata$data, .verbose = FALSE)
vis(pr, "freq")
#> Warning: Removed 38488 rows containing non-finite outside the scale range
#> (`stat_boxplot()`).

vis(pr, "freq", .type = "none")
#> Warning! Visualising 3524 points. Too many points may take a while to visualise depending on your hardware. We highly recommend you to use other types: "mean" or "boxplot"
#> Warning: Removed 38488 rows containing missing values or values outside the scale range
#> (`geom_point()`).


vis(pr, "clonotypes", 1, 2)
#> Warning: Groups with fewer than two data points have been dropped.
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_density()`).
#> `geom_smooth()` using formula = 'y ~ x'
#> Warning: Groups with fewer than two data points have been dropped.
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_density()`).

# }