Nothing
megapteraHeatmap <- function(conn, col = "gb", sort = "phylo"){
close.after <- FALSE
if ( class(conn) == "sproj" ){
conn <- dbConnect(PostgreSQL(), host = x$db[["host"]],
port = x$db[["port"]], dbname = x$db[["dbname"]],
user = x$db[["user"]], password = x$db[["password"]])
close.after <- TRUE
}
x <- "SELECT * FROM taxonomy JOIN locus USING (spec) ORDER BY spec"
x <- dbGetQuery(conn, x)
x <- x[, grep(paste("spec|_", col, sep = ""), colnames(x))]
colnames(x) <- gsub(paste("^_", col, sep = "|_"), "",
colnames(x))
colnames(x) <- gsub("_", ".", colnames(x))
rownames(x) <- x$spec
x$spec <- NULL
x <- as.matrix(x)
x[is.na(x)] <- 0
if ( col == "blocks" ){
x[grep("selected", x)] <- 1
x[grep("excluded", x)] <- 0
mode(x) <- "numeric"
}
if (sort == "phylo" ){
tax <- dbReadTaxonomy(conn)
tax <- fixNodes(ladderize(tax2tree(tax)))
x <- x[match(tax$tip.label, rownames(x)), ]
}
not <- rowSums(x) == 0
cat("\n", length(which(not)), "species missing")
write(rownames(x)[not], file = "missing.txt")
## create pdf
pdf("aaa.pdf", paper = "a4", height = 21, width = 4)
par(mai = c(0.3, 1, .2, 0))
# plot(tax, show.tip.label = FALSE, no.margin = TRUE)
if ( col == "blocks" ){
colors <- c("darkblue", "red")
} else {
colors <- c("darkblue", "yellow", rep("orange", 9),
rep("red", max(x) - 10))
}
image(t(x), xaxt = "n", yaxt = "n", col = colors)
mtext(colnames(x), side = 3, line = 0.1, at = seq(from = 0, to = 1, length.out = ncol(x)), cex = .6,
adj = .5, las = 1)
rcol <- rep("black", nrow(x))
rcol[not] <- "red"
mtext(gsub("_", " ", rownames(x)),
side = 2, line = 0.1, at = seq(from = 0, to = 1,
length.out = nrow(x)),
cex = .35,
adj = 1, las = 1, col = rcol)
dev.off()
system("open aaa.pdf")
system("open notOnGenBank.txt")
}
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