tcR (version 2.3.2)

spectratype: Spectratype

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)
# }