vis.clonal_family_tree: Visualise clonal family tree

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

Visualise clonal family tree

Description

Visualise clonal family tree

Usage

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

Arguments

.data	Single clonal family tree data from 1 cluster: 1 element from TreeStats column from 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)

# This condition can be omitted; it prevents the example from crashing
# when ClustalW or PHYLIP are not installed
if (!("step_failure_ignored" %in% class(clonal_family))) {
  vis(clonal_family[["full_clones"]][["TreeStats"]][[2]])
}

immunarch documentation built on Dec. 28, 2022, 2:59 a.m.