Visualise clonal family tree: wrapper for calling on the entire repClonalFamily output
# S3 method for clonal_family vis(.data, ...)
Clonal families from 1 or multiple samples:
Not used here.
A ggraph object.
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() #> Warning: Genes or alleles IGHV4-55 from sample full_clones not found in the reference and will be dropped! #> Probably, species argument is wrong (current value: HomoSapiens) or the data contains non-BCR genes. #> Warning: Warning! Data has more than 1 cluster! #> Clonal tree will be drawn for the 1st cluster in the 1st sample. #> To draw a tree for a specific cluster, use: #> vis(data[["sample_name"]][["TreeStats"]][[cluster_number]])