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.

To obtain all observed and reconstructed sequences for all clones, use the getAllSeqs function.

You can save the output of getAllSeqs as a fasta file using the dfToFasta 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"

# Get all sequences as a data frame
all_sequences = getAllSeqs(trees)

head(all_sequences)

## # A tibble: 6 × 6
##   clone_id node_id         node locus sequence                sequence_alignment
##      <dbl> <chr>          <int> <chr> <chr>                   <chr>             
## 1     3128 GN5SHBT02CBV0C     1 N     GAGGTGCAGCTGGTGGAGTCCG… GAGGTGCAGCTGGTGGA…
## 2     3128 GN5SHBT01B64R3     2 N     GAGGTGCAGCTGGTGGAGTCCG… GAGGTGCAGCTGGTGGA…
## 3     3128 GN5SHBT02EXTV5     3 N     GAGGTGCAGCTGGTGGAGTCCG… GAGGTGCAGCTGGTGGA…
## 4     3128 GN5SHBT08H9MGK     4 N     GAGGTGCAGCTGGTGGAGTCGG… GAGGTGCAGCTGGTGGA…
## 5     3128 GN5SHBT06FXJ8P     5 N     GAGGTGCAGCTGGTGGAGTCTG… GAGGTGCAGCTGGTGGA…
## 6     3128 GN5SHBT03CT6HZ     6 N     GAGGTGCAGCTGGTGGAGTCCG… GAGGTGCAGCTGGTGGA…

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