Nothing
plot.iC10 <-
function (x, sample.name = 1, newdata = NULL, ...)
{
par(no.readonly = TRUE)
oldpar <- par(no.readonly = TRUE)
if (!is.numeric(sample.name))
sample.name <- which(names(x$class) == sample.name)
coliCluster <- c("#FF5500", "#00EE76", "#CD3278", "#00C5CD",
"#8B0000", "#FFFF40", "#0000CD", "#FFAA00", "#EE82EE",
"#7D26CD")
cn.features <- NULL
exp.features <- NULL
if (attr(x, "classifier.type") != "Exp") {
cn.features <- x$map.cn
cn.features$Type <- "CN"
}
if (attr(x, "classifier.type") != "CN") {
exp.features <- x$map.exp
exp.features$Type <- "Exp"
}
max.grey.square <- nrow(cn.features)
features <- rbind(cn.features, exp.features)
ref <- paste("chromosome_name", attr(x, "ref"), sep="_")
features$CHROM <- features[,ref]
Pos <- c(1, which(diff(features$CHROM) != 0), nrow(features))
text.pos <- Pos + c(diff(Pos)/2, 0)
text.pos <- text.pos[-length(text.pos)]
if (!is.null(newdata)) {
tmp <- rbind(newdata$CN, newdata$Exp)
for (i in 1:10) {
if (length(which(x$class == i)) > 0) {
x$centroids[, i] <- apply(tmp[, which(x$class ==
i), drop = F], 1, mean)
}
}
}
par(mfrow = c(6, 2), mar = c(2.5, 4, 2, 2), oma = c(2, 2,
2, 2), no.readonly = TRUE)
for (i in 1:10) {
plot(x$centroids[, i], type = "h", col = coliCluster[i],
xlab = "", ylab = paste("iC", i), axes = F, ylim = range(x$centroids))
axis(2)
bottom.axis.pos <- seq(from = 1, by = 2, length = length(text.pos))
top.axis.pos <- seq(from = 2, by = 2, length = length(text.pos))
axis(1, at = text.pos[bottom.axis.pos], features$CHROM[Pos[-1]][bottom.axis.pos])
axis(3, at = text.pos[top.axis.pos], features$CHROM[Pos[-1]][top.axis.pos])
box()
if (attr(x, "classifier.type") != "Exp") {
polygon(x = rep(c(0, max.grey.square), c(2, 2)),
y = c(range(x$centroids[, i]), rev(range(x$centroids[,
i]))), density = NA, border = "lightgrey",
col = "lightgrey", ylab = paste("iC", i))
}
points(x$centroids[, i], type = "h", col = coliCluster[i],
xlab = "")
abline(v = Pos, lty = 2)
}
if (is.null(newdata)) {
plot(x$fitted[, sample.name], type = "h", col = "black",
xlab = "", ylab = "Prediction", axes = F)
axis(2)
axis(1, at = text.pos[bottom.axis.pos], features$CHROM[Pos[-1]][bottom.axis.pos])
axis(3, at = text.pos[top.axis.pos], features$CHROM[Pos[-1]][top.axis.pos])
if (attr(x, "classifier.type") != "Exp") {
polygon(x = rep(c(0, max.grey.square), c(2, 2)),
y = c(range(x$fitted[, sample.name]), rev(range(x$fitted[,
sample.name]))), density = NA, border = "lightgrey",
col = "lightgrey")
}
points(x$fitted[, sample.name], type = "h", col = "black")
abline(v = Pos, lty = 2)
barplot(x$posterior[sample.name, ], col = coliCluster,
ylim = c(0, 1), ylab = "Prob.classif.")
}
else {
plot(0, 0, type = "n", axes = F, xlab = "", ylab = "")
barplot(table(x$class), col = coliCluster, ylab = "Frequency")
}
par(oldpar, no.readonly = TRUE)
}
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