buildPhylipLineage: Infer an Ig lineage using PHYLIP

In alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

Infer an Ig lineage using PHYLIP

Description

buildPhylipLineage reconstructs an Ig lineage via maximum parsimony using the dnapars application, or maximum liklihood using the dnaml application of the PHYLIP package.

Usage

buildPhylipLineage(
  clone,
  phylip_exec,
  dist_mat = getDNAMatrix(gap = 0),
  rm_temp = FALSE,
  verbose = FALSE,
  temp_path = NULL,
  onetree = FALSE,
  branch_length = c("mutations", "distance")
)

Arguments

clone	ChangeoClone object containing clone data.
phylip_exec	absolute path to the PHYLIP dnapars executable.
dist_mat	character distance matrix to use for reassigning edge weights. Defaults to a Hamming distance matrix returned by getDNAMatrix with gap=0. If gap characters, c("-", "."), are assigned a value of -1 in dist_mat then contiguous gaps of any run length, which are not present in both sequences, will be counted as a distance of 1. Meaning, indels of any length will increase the sequence distance by 1. Gap values other than -1 will return a distance that does not consider indels as a special case.
rm_temp	if TRUE delete the temporary directory after running dnapars; if FALSE keep the temporary directory.
verbose	if FALSE suppress the output of dnapars; if TRUE STDOUT and STDERR of dnapars will be passed to the console.
temp_path	specific path to temp directory if desired.
onetree	if TRUE save only one tree.
branch_length	specifies how to define branch lengths; one of "mutations" or "distance". If set to "mutations" (default), then branch lengths represent the number of mutations between nodes. If set to "distance", then branch lengths represent the expected number of mutations per site, unaltered from PHYLIP output.

Details

buildPhylipLineage builds the lineage tree of a set of unique Ig sequences via maximum parsimony through an external call to the dnapars application of the PHYLIP package. dnapars is called with default algorithm options, except for the search option, which is set to "Rearrange on one best tree". The germline sequence of the clone is used for the outgroup.

Following tree construction using dnapars, the dnapars output is modified to allow input sequences to appear as internal nodes of the tree. Intermediate sequences inferred by dnapars are replaced by children within the tree having a Hamming distance of zero from their parent node. With the default dist_mat, the distance calculation allows IUPAC ambiguous character matches, where an ambiguous character has distance zero to any character in the set of characters it represents. Distance calculation and movement of child nodes up the tree is repeated until all parent-child pairs have a distance greater than zero between them. The germline sequence (outgroup) is moved to the root of the tree and excluded from the node replacement processes, which permits the trunk of the tree to be the only edge with a distance of zero. Edge weights of the resultant tree are assigned as the distance between each sequence.

Value

An igraph graph object defining the Ig lineage tree. Each unique input sequence in clone is a vertex of the tree, with additional vertices being either the germline (root) sequences or inferred intermediates. The graph object has the following attributes.

Vertex attributes:

• name: value in the sequence_id column of the data slot of the input clone for observed sequences. The germline (root) vertex is assigned the name "Germline" and inferred intermediates are assigned names with the format "Inferred1", "Inferred2", ....

• sequence: value in the sequence column of the data slot of the input clone for observed sequences. The germline (root) vertex is assigned the sequence in the germline slot of the input clone. The sequence of inferred intermediates are extracted from the dnapars output.

• label: same as the name attribute.

Additionally, each other column in the data slot of the input clone is added as a vertex attribute with the attribute name set to the source column name. For the germline and inferred intermediate vertices, these additional vertex attributes are all assigned a value of NA.

Edge attributes:

• weight: Hamming distance between the sequence attributes of the two vertices.

• label: same as the weight attribute.

Graph attributes:

• clone: clone identifier from the clone slot of the input ChangeoClone.

• v_gene: V-segment gene call from the v_gene slot of the input ChangeoClone.

• j_gene: J-segment gene call from the j_gene slot of the input ChangeoClone.

• junc_len: junction length (nucleotide count) from the junc_len slot of the input ChangeoClone.

  Alternatively, this function will return an phylo object, which is compatible with the ape package. This object will contain reconstructed ancestral sequences in nodes attribute.

References

1. Felsenstein J. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics. 1989 5:164-166.

2. Stern JNH, Yaari G, Vander Heiden JA, et al. B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes. Sci Transl Med. 2014 6(248):248ra107.

See Also

Takes as input a ChangeoClone. Temporary directories are created with makeTempDir. Distance is calculated using seqDist. See [igraph](http://www.rdocumentation.org/packages/igraph/topics/aaa-igraph-package) and [igraph.plotting](http://www.rdocumentation.org/packages/igraph/topics/plot.common) for working with igraph graph objects.

Examples

## Not run: 
# Preprocess clone
db <- subset(ExampleDb, clone_id == 3138)
clone <- makeChangeoClone(db, text_fields=c("sample_id", "c_call"), 
                          num_fields="duplicate_count")

# Run PHYLIP and process output
phylip_exec <- "~/apps/phylip-3.695/bin/dnapars"
graph <- buildPhylipLineage(clone, phylip_exec, rm_temp=TRUE)

# Plot graph with a tree layout
library(igraph)
plot(graph, layout=layout_as_tree, vertex.label=V(graph)$c_call, 
     vertex.size=50, edge.arrow.mode=0, vertex.color="grey80")

# To consider each indel event as a mutation, change the masking character 
# and distance matrix
clone <- makeChangeoClone(db, text_fields=c("sample_id", "c_call"), 
                          num_fields="duplicate_count", mask_char="-")
graph <- buildPhylipLineage(clone, phylip_exec, dist_mat=getDNAMatrix(gap=-1), 
                            rm_temp=TRUE)

## End(Not run)

alakazam documentation built on Sept. 30, 2023, 9:07 a.m.