vis.clonal_family: Visualise clonal family tree: wrapper for calling on the...

In immunomind/immunarch: Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires

Visualise clonal family tree: wrapper for calling on the entire repClonalFamily output

Description

Visualise clonal family tree: wrapper for calling on the entire repClonalFamily output

Usage

## S3 method for class 'clonal_family'
vis(.data, ...)

Arguments

.data	Clonal families from 1 or multiple samples: repClonalFamily output.
...	Not used here.

Value

A ggraph object.

Examples

data(bcrdata)
bcr_data <- bcrdata$data

clonal_family <- bcr_data %>%
  seqCluster(seqDist(bcr_data), .fixed_threshold = 3) %>%
  repGermline(.threads = 1) %>%
  repAlignLineage(.min_lineage_sequences = 2, .align_threads = 2, .nofail = TRUE) %>%
  repClonalFamily(.threads = 1, .nofail = TRUE) %>%
  vis()

immunomind/immunarch documentation built on March 20, 2024, 12:01 p.m.