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plotMAhex <- function (MA, array = 1, xlab = "A", ylab = "M",
main = colnames(MA)[array],
xlim = NULL, ylim = NULL, status = NULL,
values, pch, col, cex, nbin=40,
zero.weights = FALSE,
style = "colorscale", legend = 1.2, lcex = 1,
minarea = 0.04, maxarea = 0.8, mincnt = 2,
maxcnt = NULL, trans = NULL, inv = NULL,
colorcut = NULL,
border = NULL, density = NULL, pen = NULL,
colramp = function(n){ LinGray(n,beg = 90,end = 15) },
newpage = TRUE, type = c("p", "l", "n"),
xaxt = c("s", "n"), yaxt = c("s", "n"),
verbose = getOption("verbose"))
{
if (!requireNamespace("marray", quietly = TRUE))
stop("cannot process objects without package marray")
if (!requireNamespace("limma", quietly = TRUE))
stop("cannot process objects without package limma")
if(is.null(main))main <- ""
switch(class(MA),marrayRaw={
x <- marray::maA(MA[,array])
y <- marray::maM(MA[,array])
w <- marray::maW(MA[,array])
},RGList = {
MA <- limma::MA.RG(MA[, array])
array <- 1
x <- MA$A
y <- MA$M
w <- MA$w
}, MAList = {
x <- as.matrix(MA$A)[, array]
y <- as.matrix(MA$M)[, array]
if (is.null(MA$weights))
w <- NULL
else
w <- as.matrix(MA$weights)[, array]
}, list = {
if (is.null(MA$A) || is.null(MA$M))
stop("No data to plot")
x <- as.matrix(MA$A)[, array]
y <- as.matrix(MA$M)[, array]
if (is.null(MA$weights))
w <- NULL
else
w <- as.matrix(MA$weights)[, array]
}, MArrayLM = {
x <- MA$Amean
y <- as.matrix(MA$coefficients)[, array]
if (is.null(MA$weights))
w <- NULL
else
w <- as.matrix(MA$weights)[, array]
}, matrix = {
narrays <- ncol(MA)
if (narrays < 2)
stop("Need at least two arrays")
if (narrays > 5)
x <- apply(MA, 1, median, na.rm = TRUE)
else
x <- rowMeans(MA, na.rm = TRUE)
y <- MA[, array] - x
w <- NULL
}, ExpressionSet = {
if (!requireNamespace("Biobase", quietly = TRUE))
stop("cannot process ExpressionSet objects without package Biobase")
narrays <- ncol(Biobase::exprs(MA))
if (narrays < 2)
stop("Need at least two arrays")
if (narrays > 5)
x <- apply(Biobase::exprs(MA), 1, median, na.rm = TRUE)
else
x <- rowMeans(Biobase::exprs(MA), na.rm = TRUE)
y <- Biobase::exprs(MA)[, array] - x
w <- NULL
if (missing(main))
main <- colnames(Biobase::exprs(MA))[array]
}, AffyBatch = {
if (!requireNamespace("Biobase", quietly = TRUE) ||
!requireNamespace("affy", quietly = TRUE))
stop("cannot process AffyBatch objects without package Biobase and affy")
narrays <- ncol(Biobase::exprs(MA))
if (narrays < 2)
stop("Need at least two arrays")
if (narrays > 5)
x <- apply(log2(Biobase::exprs(MA)), 1, median, na.rm = TRUE)
else
x <- rowMeans(log2(Biobase::exprs(MA)), na.rm = TRUE)
y <- log2(Biobase::exprs(MA)[, array]) - x
w <- NULL
if (missing(main))
main <- colnames(Biobase::exprs(MA))[array]
}, stop("MA is invalid object"))
if (!is.null(w) && !zero.weights) {
i <- is.na(w) | (w <= 0)
y[i] <- NA
}
if (is.null(xlim))
xlim <- range(x, na.rm = TRUE)
if (is.null(ylim))
ylim <- range(y, na.rm = TRUE)
hbin <- hexbin(x,y,xbins=nbin,xbnds=xlim,ybnds=ylim, IDs = TRUE)
hp <- plot(hbin, legend=legend, xlab = xlab, ylab = ylab, main = main,
type='n', newpage=newpage)
## plot the hexagons
pushHexport(hp$plot.vp)
if(is.null(maxcnt)) maxcnt <- max(hbin@count)
if(is.null(colorcut)) colorcut<-seq(0, 1, length = min(17, maxcnt))
grid.hexagons(hbin, style=style, minarea = minarea, maxarea = maxarea,
mincnt = mincnt, maxcnt= maxcnt, trans = trans,
colorcut = colorcut, density = density, border = border,
pen = pen, colramp = colramp)
if (is.null(status) || all(is.na(status))) {
if (missing(pch))
pch <- 16
if (missing(cex))
cex <- 0.3
if (missing(col)) {
clrs <- colramp(length(colorcut)-1)
col <- clrs[1]
}
pp <- inout.hex(hbin,mincnt)
grid.points(x[pp], y[pp], pch = pch[[1]],
gp=gpar(cex = cex[1], col=col, fill=col))
}
else {
if (missing(values)) {
if (is.null(attr(status, "values")))
values <- names(sort(table(status), decreasing = TRUE))
else
values <- attr(status, "values")
}
sel <- !(status %in% values)
nonhi <- any(sel)
if (nonhi) grid.points(x[sel], y[sel], pch = 16, gp=gpar(cex = 0.3))
nvalues <- length(values)
if (missing(pch)) {
if (is.null(attr(status, "pch")))
pch <- rep(16, nvalues)
else
pch <- attr(status, "pch")
}
if (missing(cex)) {
if (is.null(attr(status, "cex"))) {
cex <- rep(1, nvalues)
if (!nonhi)
cex[1] <- 0.3
}
else
cex <- attr(status, "cex")
}
if (missing(col)) {
if (is.null(attr(status, "col"))) {
col <- nonhi + 1:nvalues
}
else
col <- attr(status, "col")
}
pch <- rep(pch, length = nvalues)
col <- rep(col, length = nvalues)
cex <- rep(cex, length = nvalues)
for (i in 1:nvalues) {
sel <- status == values[i]
grid.points(x[sel], y[sel], pch = pch[[i]], gp=gpar(cex = cex[i], col = col[i]))
}
}
popViewport()
if (legend > 0) {
inner <- getPlt(hp$plot.vp, ret.unit="inches", numeric=TRUE)[1]
inner <- inner/hbin@xbins
ysize <- getPlt(hp$plot.vp, ret.unit="inches", numeric=TRUE)[2]
pushViewport(hp$legend.vp)
grid.hexlegend(legend, ysize=ysize, lcex = lcex, inner = inner,
style= style, minarea= minarea, maxarea= maxarea,
mincnt= mincnt, maxcnt= maxcnt,
trans=trans, inv=inv,
colorcut = colorcut,
density = density, border = border, pen = pen,
colramp = colramp)
#if (is.list(pch))
# legend(x = xlim[1], y = ylim[2], legend = values,
# fill = col, col = col, cex = 0.9)
#else legend(x = xlim[1], y = ylim[2], legend = values,
# pch = pch, , col = col, cex = 0.9)
popViewport()
}
invisible(list(hbin = hbin, plot.vp = hp$plot.vp, legend.vp = hp$legend.vp))
}
hexMA.loess <- function(pMA, span = .4, col = 'red', n = 200, ...)
{
fit <- hexVP.loess(pMA$hbin, pMA$plot.vp, span = span, col = col, n = n, ...)
invisible(fit)
}
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