Nothing
image.vhica <-
function (x, element = "", H1.test = "bilat", treefile = NULL,
skip.void = FALSE, species = NULL, p.threshold = 0.05, p.adjust.method = "bonferroni",
ncolors = 1024, main = element, threshcol = 0.1, colsqueeze=1, species.font.family="mono", species.font.cex=1,
max.spname.length=10, ...)
{
op <- par(no.readonly = TRUE)
tree <- .prepare.phylo(treefile)
if (!"phylo" %in% class(tree)) {
species <- .check.species(x, user.species = species)
tree <- list(tip.label = species)
}
else {
species <- .check.species(x, user.species = species,
tree.species = tree$tip.label)
}
elements <- .element.present(x, element, species = tree$tip.label,
skip.void = skip.void)
if(is.null(elements)) {
stop("Element ", element, " cannot be found. Nothing to plot.")
}
if (length(tree) > 1 && skip.void) {
missing.species <- tree$tip.label[!tree$tip.label %in%
sapply(strsplit(elements, ".", fixed = TRUE), function(el) el[1])]
tree <- ape::drop.tip(tree, missing.species)
species <- species[species %in% tree$tip.label]
}
stats <- .stat.matrix(vhica.obj = x, element = element, elements = elements,
p.adjust.method = p.adjust.method, H1.test = H1.test)
thresh <- NULL
col.range <- c(-0.5, 0.5)
if (H1.test != "greater") {
thresh <- c(thresh, -abs(log10(p.threshold)))
col.range[1] <- -5
}
if (H1.test != "lower") {
thresh <- c(thresh, abs(log10(p.threshold)))
col.range[2] <- 5
}
cols <- .make.col.obj(n = ncolors, min.col = "red", max.col = "blue",
threshold = thresh, range = col.range, threshcol = threshcol, colsqueeze=colsqueeze)
layout(matrix(1:4, nrow = 2), widths = c(0.3, 0.7), heights = c(0.3,
0.7))
.plot.caption(col.obj = cols, main = element, p.adjust.method = p.adjust.method,
thresh.lines = thresh)
if ("phylo" %in% class(tree)) {
.plot.phylo(tree, species, horizontal = TRUE)
}
else {
frame()
}
if ("phylo" %in% class(tree)) {
.plot.phylo(tree, species)
}
else {
frame()
}
.plot.matrix(pmatrix = stats, species = species, elements = elements,
col.obj = cols, species.font.family=species.font.family, species.font.cex=species.font.cex,
max.spname.length=max.spname.length, ...)
layout(1)
par(op)
# There is probably a more elegant way to do this
dS <- matrix(NA, ncol=ncol(stats), nrow=nrow(stats))
colnames(dS) <- colnames(stats)
rownames(dS) <- rownames(stats)
dS[as.matrix(x$div[x$div$seq==element, c("sp1","sp2")])] <- x$div$dS[x$div$seq==element]
dS[as.matrix(x$div[x$div$seq==element, c("sp2","sp1")])] <- x$div$dS[x$div$seq==element]
ans <- list(name = element, tree = tree, species = species, elements = elements,
stats = stats, thresh=thresh, dS=dS)
class(ans) <- c("vhicaimage", class(ans))
return(invisible(ans))
}
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