Visualise clonal family tree — vis.clonal_family

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

# \dontrun{
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)
#> repAlignLineage requires Clustal W app to be installed!
#> Please download it from here: http://www.clustal.org/download/current/
#> or install it with your system package manager (such as apt or dnf).

# 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]])
}
# }