1 | BoxplotNorm_oligo(est_noctrls, strt = NULL, nd = NULL, parameters, conditions = NULL, colors = NULL)
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est_noctrls |
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strt |
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nd |
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parameters |
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conditions |
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colors |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 | ##---- Should be DIRECTLY executable !! ----
##-- ==> Define data, use random,
##-- or do help(data=index) for the standard data sets.
## The function is currently defined as
function (est_noctrls, strt = NULL, nd = NULL, parameters, conditions = NULL,
colors = NULL)
{
lab <- colnames(est_noctrls)
if (is.null(strt) & is.null(nd)) {
strt <- 1
nd <- length(ncol(est_noctrls))
}
else if (is.null(strt)) {
strt <- 1
}
else if (is.null(nd)) {
nd <- length(ncol(est_noctrls))
}
if (is.null(conditions)) {
boxplot(est_noctrls, main = "Boxplot RMA all probe sets",
xaxt = "n")
axis(1, at = 1:length(lab), labels = lab, cex.axis = parameters$ce,
las = 2)
}
else if (is.null(colors)) {
CondNames <- mixedsort(lab)
CondTable <- data.frame(CondNames, conditions)
conditions.o <- CondTable[match(lab, CondTable$CondNames),
"conditions"]
list1 <- unique(as.character(sort(conditions.o)))
ColVect <- c(brewer.pal(8, "Dark2"), brewer.pal(12, "Paired"))
list2 <- ColVect[1:length(unique(conditions))]
map = setNames(list2, list1)
colors <- map[conditions.o]
boxplot(est_noctrls, main = "Boxplot RMA all probe sets",
xaxt = "n", col = colors)
axis(1, at = 1:length(lab), labels = lab, cex.axis = parameters$ce,
las = 2)
legend("topright", legend = list1, cex = 0.5, fill = list2)
}
else {
CondNames <- mixedsort(lab)
CondTable <- data.frame(CondNames, conditions)
conditions.o <- CondTable[match(lab, CondTable$CondNames),
"conditions"]
list1 <- unique(as.character(sort(conditions.o)))
list2 <- colors
map = setNames(list2, list1)
colors <- map[conditions.o]
boxplot(est_noctrls, main = "Boxplot RMA all probe sets",
xaxt = "n", col = colors)
axis(1, at = 1:length(lab), labels = lab, cex.axis = parameters$ce,
las = 2)
legend("topright", legend = list1, cex = 0.5, fill = list2)
}
}
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