network {RepertoiR} | R Documentation |
Sequences distance network
Description
Computes pairwise string distances among repertoire's sequences and visualize similar pairs as connected nodes, each sized by its frequency.
Usage
network(dataset, by, nrow, method, ...)
Arguments
dataset |
A matrix or a data frame includes row names which are used as the compared sequences. Data set's numeric values determine node-size. |
by |
Index of column to set its values as node-size. first column is default (1). |
nrow |
Number of nodes to display. Default is 1000 nodes. |
method |
stringdist method to perform for distance dissimilarity calculation: "osa", "lv", "dl", "hamming", "lcs", "qgram", "cosine", "jaccard", "jw", "soundex". Default is Levenshtein distance ("lv"). |
... |
Any additional arguments needed by the specialized methods. |
Value
No return value.
Examples
aa <- c(
"G", "A", "V", "L", "I", "P", "F", "Y", "W", "S",
"T", "N", "Q", "C", "M", "D", "E", "H", "K", "R"
)
data <- matrix(rexp(1 / 2, n = 1000), ncol = 4)
cons <- sample(aa, 10)
aavec <- c()
while (length(aavec) < nrow(data)) {
aaseq <- cons
index <- sample(length(aaseq), sample(length(aaseq) / 3, 1))
aaseq[index] <- sample(aa, length(index), replace = TRUE)
aaseq <- paste0(aaseq, collapse = "")
aavec <- unique(append(aavec, aaseq))
}
rownames(data) <- aavec
colnames(data) <- LETTERS[1:ncol(data)]
network(data, by = 3, nrow = 100)
[Package RepertoiR version 0.0.1 Index]