spectratype: Spectratype

In tcR: Advanced Data Analysis of Immune Receptor Repertoires

Description

Plot a spectratype plot - a histogram of read counts / umi counts by CDR3 length.

Usage

spectratype(
  .data,
  .quant = c("read.count", "umi.count", "id"),
  .gene = "V",
  .plot = T,
  .main = "Spectratype",
  .legend = "Gene segment",
  .labs = c("CDR3 length", NA)
)

Arguments

.data	tcR data frame.
.quant	Either "read.count" or "umi.count" for choosing the corresponding columns, or "id" to compute avoid using counts.
.gene	Either NA for not using genes, "V" or "J" for corresponding genes.
.plot	If T than plot the spectratype plot, otherwise return a table with data for lengths and counts.
.main	Main title.
.legend	Legend title.
.labs	Character vector of length 2 for x-lab and y-lab.

Examples

## Not run: 
data(twb)
tmp = twb[[1]]
spectratype(tmp)
spectratype(tmp, .quant = "id", .plot = T, .gene = 'V')
spectratype(tmp, .quant = "read.count", .plot = F)

## End(Not run)

tcR documentation built on July 2, 2020, 3:18 a.m.