-## DNA.R (2011-03-16)
+## DNA.R (2012-06-19)
## Manipulations and Comparisons of DNA Sequences
-## Copyright 2002-2011 Emmanuel Paradis
+## Copyright 2002-2012 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
nms <- names(x)
if (n == 1) {
cat("1 DNA sequence in binary format stored in a list.\n\n")
- cat("Sequence length:", length(x[[1]]), "\n\n")
+ nTot <- length(x[[1]])
+ cat("Sequence length:", nTot, "\n\n")
cat("Label:", nms, "\n\n")
} else {
cat(n, "DNA sequences in binary format stored in a list.\n\n")
tmp <- unlist(lapply(x, length))
- mini <- min(tmp)
- maxi <- max(tmp)
+ nTot <- sum(tmp)
+ mini <- range(tmp)
+ maxi <- mini[2]
+ mini <- mini[1]
if (mini == maxi)
cat("All sequences of same length:", maxi, "\n")
else {
}
cat("\nLabels:", paste(nms, collapse = " "), TAIL)
}
- } else if (is.matrix(x)) {
- nd <- dim(x)
- nms <- rownames(x)
- cat(nd[1], "DNA sequences in binary format stored in a matrix.\n\n")
- cat("All sequences of same length:", nd[2], "\n")
- TAIL <- "\n\n"
- if (printlen < nd[1]) {
- nms <- nms[1:printlen]
- TAIL <- "...\n\n"
- }
- cat("\nLabels:", paste(nms, collapse = " "), TAIL)
} else {
- cat("1 DNA sequence in binary format stored in a vector.\n\n")
- cat("Sequence length:", length(x), "\n\n")
+ nTot <- length(x)
+ if (is.matrix(x)) {
+ nd <- dim(x)
+ nms <- rownames(x)
+ cat(nd[1], "DNA sequences in binary format stored in a matrix.\n\n")
+ cat("All sequences of same length:", nd[2], "\n")
+ TAIL <- "\n\n"
+ if (printlen < nd[1]) {
+ nms <- nms[1:printlen]
+ TAIL <- "...\n\n"
+ }
+ cat("\nLabels:", paste(nms, collapse = " "), TAIL)
+ } else {
+ cat("1 DNA sequence in binary format stored in a vector.\n\n")
+ cat("Sequence length:", nTot, "\n\n")
+ }
}
- cat("Base composition:\n")
- print(round(base.freq(x), digits))
+ if (nTot <= 1e6) {
+ cat("Base composition:\n")
+ print(round(base.freq(x), digits))
+ } else cat("More than 1 million nucleotides: not printing base composition\n")
}
as.DNAbin <- function(x, ...) UseMethod("as.DNAbin")
._cs_ <- c("a", "g", "c", "t", "r", "m", "w", "s", "k",
- "y", "v", "h", "d", "b", "n", "-", "?")
+ "y", "v", "h", "d", "b", "n", "-", "?")
._bs_ <- c(136, 72, 40, 24, 192, 160, 144, 96, 80,
48, 224, 176, 208, 112, 240, 4, 2)
as.matrix = FALSE)
{
MODELS <- c("RAW", "JC69", "K80", "F81", "K81", "F84", "T92", "TN93",
- "GG95", "LOGDET", "BH87", "PARALIN", "N", "TS", "TV")
+ "GG95", "LOGDET", "BH87", "PARALIN", "N", "TS", "TV",
+ "INDEL", "INDELBLOCK")
imod <- pmatch(toupper(model), MODELS)
if (is.na(imod))
stop(paste("'model' must be one of:",
paste("\"", MODELS, "\"", sep = "", collapse = " ")))
if (imod == 11 && variance) {
- warning("computing variance temporarily not available for model BH87.")
+ warning("computing variance not available for model BH87")
variance <- FALSE
}
- if (gamma && imod %in% c(1, 5:7, 9:15)) {
+ if (gamma && imod %in% c(1, 5:7, 9:17)) {
warning(paste("gamma-correction not available for model", model))
gamma <- FALSE
}
n <- dim(x)
s <- n[2]
n <- n[1]
+
if (imod %in% c(4, 6:8)) {
BF <- if (is.null(base.freq)) base.freq(x) else base.freq
} else BF <- 0
+
+ if (imod %in% 16:17) pairwise.deletion <- TRUE
+
if (!pairwise.deletion) {
keep <- .C("GlobalDeletionDNA", x, n, s,
rep(1L, s), PACKAGE = "ape")[[4]]
- x <- x[, as.logical(keep)]
+ x <- x[, as.logical(keep)]
s <- dim(x)[2]
}
Ndist <- if (imod == 11) n*n else n*(n - 1)/2
y <- integer(N <- length(x))
ncl <- length(what)
col <- rep(col, length.out = ncl)
+ brks <- 0.5:(ncl + 0.5)
sm <- 0L
for (i in ncl:1) {
k <- ._bs_[._cs_ == what[i]]
sel <- which(x == k)
- if (ll <- length(sel)) {
+ if (L <- length(sel)) {
y[sel] <- i
- sm <- sm + ll
+ sm <- sm + L
} else {
what <- what[-i]
col <- col[-i]
+ brks <- brks[-i]
}
}
dim(y) <- dx
co <- c(bg, col)
leg.txt <- c(toupper(what), "others")
leg.co <- c(col, bg)
+ brks <- c(-0.5, brks)
}
yaxt <- if (show.labels) "n" else "s"
- image(1:s, 1:n, t(y), col = co, xlab = xlab,
- ylab = ylab, yaxt = yaxt, ...)
+ graphics::image.default(1:s, 1:n, t(y), col = co, xlab = xlab,
+ ylab = ylab, yaxt = yaxt, breaks = brks, ...)
if (show.labels)
mtext(rownames(x), side = 2, line = 0.1, at = 1:n,
cex = cex.lab, adj = 1, las = 1)