Public repertoire visualisation

Visualise public clonotype frequencies.

Usage

vis_public_frequencies(
  .data,
  .by = NA,
  .meta = NA,
  .type = c("boxplot", "none", "mean")
)

Arguments

.data

Public repertoire - an output from the pubRep function.

.by

Pass NA if you want to plot samples without grouping.

You can pass a character vector with one or several column names from ".meta" to group your data before plotting. In this case you should provide ".meta".

You can pass a character vector that exactly matches the number of samples in your data, each value should correspond to a sample's property. It will be used to group data based on the values provided. Note that in this case you should pass NA to ".meta".

.meta

A metadata object. An R dataframe with sample names and their properties, such as age, serostatus or hla.

.type

Character. Either "boxplot" for plotting distributions of frequencies, "none" for plotting everything, or "mean" for plotting average values only.

Value

A ggplot2 object.

Examples

# \dontrun{
data(immdata)
immdata$data <- lapply(immdata$data, head, 500)
pr <- pubRep(immdata$data, .verbose = FALSE)
vis(pr, "freq", .type = "boxplot")
#> Warning: Removed 64256 rows containing non-finite outside the scale range
#> (`stat_boxplot()`).

vis(pr, "freq", .type = "none")
#> Warning! Visualising 5884 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 64256 rows containing missing values or values outside the scale range
#> (`geom_point()`).

vis(pr, "freq", .type = "mean")

vis(pr, "freq", .by = "Status", .meta = immdata$meta)
#> Warning: Removed 64256 rows containing non-finite outside the scale range
#> (`stat_boxplot()`).

# }