## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
# library(dowser)
# 
# data(ExampleClones)
# 
# # Collapse nodes with identical sequences. This will
# trees = collapseNodes(ExampleClones[1:2,])
# 
# # Plot trees with node ID numbers
# plots = plotTrees(trees, tips="c_call", tipsize=2, node_nums=TRUE, labelsize=7)
# 
# plots[[1]]
# 
# sequence = getNodeSeq(trees, node=50, clone=3128)
# 
# print(sequence)
# 
# # Get all sequences as a data frame
# all_sequences = getAllSeqs(trees)
# 
# head(all_sequences)
# 

## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
# 
# # Save all sequences as a fasta file
# dfToFasta(all_sequences, file="all_sequences.fasta", id="node_id", columns=c("clone_id","locus"))
#