| imgplot {DAAGbio} | R Documentation |
Image plot of spotted expression array data
Description
Creates an image of graduated colors that represent the
values of a statistic for each spot on a spotted microarray.
By default, the only the 5
shown. The initial version was based on plot.spatial
in the sma package.
Usage
imgplot(z = DAAGbio::coralRG$R[, 1], layout = DAAGbio::coralRG$printer, crit1 = 0.05,
crit2 = crit1, key.side=2,
lohi.colors = c("#9E0142", "#D53E4F", "#F46D43", "#FDAE61", "#ABDDA4",
"#66C2A5", "#3288BD", "#5E4FA2"), nacolor = "#FFFF00",
boxplot.side = 1, split = "quantiles")
Arguments
z |
values to be plotted |
layout |
layout of spots, in the order (rows of grids, columns of grids, rows of spots in a grid, columns in a grid) |
crit1 |
Choose the lower threshold to include this proportion at the high end |
crit2 |
Choose the upper threshold to include this proportion of values at the low end |
key.side |
Side on which the color key should appear |
lohi.colors |
Graduated sequence of colors |
nacolor |
Use this color for |
boxplot.side |
Show boxplot on this side of figure region |
split |
Specify |
Value
A plot is created on the current graphics device
Author(s)
J. H. Maindonald
Examples
## The function is currently defined as
function (z=DAAGbio::coralRG$R[,1], layout=cDAAGbio::oralRG$printer, crit1 = 0.05,
crit2 = crit1, key.side=2,
lohi.colors=c("#9E0142","#D53E4F","#F46D43","#FDAE61",
"#ABDDA4","#66C2A5","#3288BD","#5E4FA2"),
nacolor="#FFFF00", boxplot.side=1, split="quantiles")
{
"block2matrix" <-
function(z, sr=3, sc=2, gr=2, gc=2){
## Assumes that values in the vector z are in row major
## order within blocks of dimension sr x sc, with blocks
## in row major order within a gr x gc array of grids.
## Elements in the vector that is returned are in row
## major order wrt the sr*gr x sc*gc matrix of values on
## the slide. (It is given the dimensions of a matrix.)
xy <- array(z, dim=c(sc, sr, gc, gr))
xy <- aperm(xy, c(1,3,2,4))
dim(xy) <- c(sc*gc, gr*sr)
xy}
quantile.na <- function (z, ...)
{
tmp <- !(is.na(z) | is.infinite(z))
quantile(z[tmp], ...)
}
length.na <- function (z, ...)
{
tmp <- !(is.na(z) | is.infinite(z))
length(z[tmp], ...)
}
if(is.matrix(z))warning("z is a matrix, You probably want a column vector")
bplot <- function(z, boxplot.side=1){
xrange <- range(z,na.rm=TRUE)
iqr <- diff(quantile(xrange, c(.25,.75)))
bwex <- diff(xrange)/(3*iqr)
xhi <- max(z,na.rm=TRUE)
xusr <- par()$usr[c(1:2)]
xpos=pretty(z[!is.na(z)], n=5)
z <- xusr[1]+(z-xrange[1])*diff(xusr)/diff(xrange)
newpos <- xusr[1]+(xpos-xrange[1])*diff(xusr)/diff(xrange)
par(xpd=TRUE)
atvert <- switch(boxplot.side, par()$usr[3]-par()$cxy[2]*0.8,
"", par()$usr[4]+par()$cxy[2]*0.8, "")
if(atvert!=""){
boxplot(z, at=atvert, boxwex=bwex, add=TRUE, horizontal=TRUE, xaxt="n")
axis(side=boxplot.side, line=1.5,
at=newpos, labels=xpos, cex.axis=0.75, mgp=c(2, 0.5, 0))
}
par(xpd=FALSE)
}
if (crit1 >= 1)
crit1 <- crit1/(length.na(z))
if (crit2 >= 1)
crit2 <- crit2/(length.na(z))
tmpind <- (z > quantile.na(z, probs = 1 - crit2)) | (z <
quantile.na(z, probs = crit1))
n <- prod(unlist(layout))
n.all <- length(z)
n.na <- sum(is.na(z))
nhalf <- length(lohi.colors)%/%2
n2 <- 2*nhalf
n.one <- length(lohi.colors)
plo <- crit1*(0:nhalf)/nhalf
phi <- 1-crit2*(nhalf:0)/nhalf
quiles1 <- quantile.na(z, plo)
quiles2 <- quantile.na(z, phi)
if(split=="intervals"){
quiles1[2:nhalf] <- quiles1[1]+(quiles1[nhalf+1]-quiles1[1])*
(1:(nhalf-1))/nhalf
quiles2[2:nhalf] <- quiles2[1]-(quiles2[nhalf+1]-quiles2[1])*
((nhalf-1):1)/nhalf
plo[-1] <- sapply(quiles1[-1],
function(x, z)sum(z<=x, na.rm=TRUE)/length.na(z), z=z)
phi[-1] <- sapply(quiles2[-1],
function(x, z)sum(z<=x, na.rm=TRUE)/length.na(z), z=z)
}
if(crit1+crit2<1){
quiles <- c(quiles1,quiles2)
frac <- c(plo, phi)
colpal <- c(lohi.colors[1:nhalf],"#FFFFFF",
lohi.colors[(n.one-nhalf+1):(n.one)])
midbreak <- TRUE
}
else {colpal <- lohi.colors
midbreak <- FALSE
quiles <- quantile.na(z, (0:n.one)/n.one)
frac <- c(plo, phi[-1])
}
dups <- duplicated(quiles)
if(any(dups)){
cats <- seq(along=quiles[-1])
filledcats <- cats[!dups]
cutcats <- as.integer(cut(z, quiles[!dups], include.lowest=TRUE))
fullm <- filledcats[cutcats]}
else fullm <- as.integer(cut(z, quiles, include.lowest=TRUE))
n.one <- length(colpal)
nrects <- length(quiles)
if(any(is.na(z))){
nacat <- TRUE
fullm[is.na(fullm)] <- max(unique(fullm[!is.na(fullm)]))+1
colpal <- c(colpal, nacolor)
}
else nacat <- FALSE
if ((length(as.vector(z)) != n) & (!is.null(names(z)))) {
y <- fullm[tmpind]
fullm <- rep(NA, n)
fullm[as.integer(names(y))] <- y
}
else fullm[!tmpind] <- NA
if ((length(as.vector(z)) != n) & (is.null(names(z)))) {
stop(paste("Error: Length of vector is different from total number\n",
"of spots and vector has no row.name.\n"))
}
#################################################################
gc <- layout$ngrid.c
gr <- layout$ngrid.r
sc <- layout$nspot.c
sr <- layout$nspot.r
full <- block2matrix(fullm, sr, sc, gr, gc)
image(1:ncol(full), 1:nrow(full), t(full), axes = FALSE,
xlab = "", ylab = "", col=colpal)
box()
abline(v = ((gr - 1):1) * (sr) + 0.5)
abline(h = (1:(gc - 1)) * (sc) + 0.5)
#################################################################
if(boxplot.side%in%c(1,3))bplot(z, boxplot.side=boxplot.side)
if(key.side%in%c(2,4)){
chw <- par()$cxy[1]
barwid <- 0.75*chw
if(key.side==2){
x0 <- par()$usr[1]-chw-barwid
xcutpos <- x0 - 0.4*chw
xquilepos <- x0+barwid+0.55*chw
srt <- 90
}
else {
x0 <- par()$usr[2]+chw
xcutpos <- x0 + barwid + 0.4*chw
xquilepos <- x0-0.4*chw
srt <- -90
}
yvals2 <- seq(from=par()$usr[3], to=par()$usr[4],
length=n2+midbreak+2*nacat+1)[-(n2+midbreak+2*nacat+1)]
eps2 <- diff(yvals2[1:2])
if(nacat){
nlast <- length(yvals2)
nclast <- length(colpal)
rect(x0, yvals2[nlast], x0+barwid, yvals2[nlast]+eps2,
col=colpal[nclast], xpd=TRUE)
text(x0+0.5*barwid, yvals2[nlast]+0.5*eps2, "NA",
xpd=TRUE, srt=srt)
yvals2 <- yvals2[-((nlast-1):nlast)]
colpal <- colpal[-nclast]
}
if(!midbreak){
rect(x0, yvals2, x0+barwid, yvals2+eps2,
col=colpal, xpd=TRUE)
text(xcutpos, c(yvals2[1],yvals2+eps2),
paste(signif(quiles,3)), srt=srt, xpd=TRUE, cex=0.8)
text(xquilepos, yvals2[1], "(0%)", srt=srt, xpd=TRUE, cex=0.65)
fracs <- frac[-c(1, length(frac))]
text(xquilepos, yvals2[-1],
paste("(",round(fracs*100,2),")",sep=""),
srt=srt, xpd=TRUE, cex=0.65)
text(xquilepos, yvals2[length(yvals2)]+eps2, "(100%)", srt=srt,
xpd=TRUE, cex=0.65)
}
else {rect(x0, yvals2[1:nhalf], x0+barwid, yvals2[1:nhalf]+eps2,
col=colpal[1:nhalf], xpd=TRUE)
rect(x0, yvals2[(nhalf+2):(2*nhalf+1)], x0+barwid,
yvals2[(nhalf+2):(2*nhalf+1)]+eps2,
col=colpal[(nhalf+2):(2*nhalf+1)], xpd=TRUE)
text(xcutpos, yvals2[1:(nhalf+1)],
paste(signif(quiles1,3)), srt=srt, xpd=TRUE, cex=0.8)
text(xquilepos, yvals2[2:(nhalf+1)],
paste("(",round(plo[-1]*100,2),")",sep=""), srt=srt,
xpd=TRUE, cex=0.65)
text(xquilepos, yvals2[1], "(0%)", srt=srt, xpd=TRUE, cex=0.65)
text(xcutpos,
c(yvals2[(nhalf+2):(2*nhalf+1)], yvals2[2*nhalf+1]+eps2),
paste(signif(quiles2,3)), srt=srt, xpd=TRUE, cex=0.8)
text(xquilepos, yvals2[(nhalf+2):(2*nhalf+1)],
paste("(",round(phi[-length(phi)]*100,2),")",sep=""),
srt=srt, xpd=TRUE, cex=0.65)
text(xquilepos, yvals2[2*nhalf+1]+eps2, "(100%)", srt=srt,
xpd=TRUE, cex=0.65)
}
}
invisible()
}
[Package DAAGbio version 0.63-4 Index]