Reconstruct Intermediate Sequences¶
Dowser automatically reconstructs intermediate sequences as part of the getTrees
function. These are stored in the nodes
list contained in each phylo
object.
First, collapse internal nodes with identical sequences using the collapesNodes
. This will significantly clean up the visualization. You could alternatively run getTrees
with collapse=TRUE
. Then, visualize the trees using plotTrees
but with the node_nums
parameter set. This will display the ID number of each internal node.
To obtain the IMGT-gapped sequence for each reconstructed node, specify the clone ID and node number in the getNodeSeq
function.
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)
## N
## "GAGGTGCAGCTGGTGGAGTCTGGGGGA...GGCTTGGTVCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTC............AGTGAYTATGCCATGAGCTGGTTCCGCCAGGCTCCAGGGAAGGGKCTGGAGTGGGTGGGTTTCATTAGAAGCAGACGTTTTGGTGGGACGCCGGACTACGCCGCGTCAGTGAGA...GACAGATTCACCATTTCAAGAGACGATTCCAAAAGCATCGCCTATCTGCAAATGAACAGCCTGAAAACCGAGGACACAGCCGTGTATTTTTGTAGTAGAGATCTCGCGGTTATATCCACAATAGCTGGTACTAACTGGTTCGACCCCAGGGGCCAGGGAGCCCTGGTCACCGTCTCCTCAGNN"