plot.expr {permax} | R Documentation |
Represents values in the rows of a matrix as colored rectangles in an image plot
plot.expr(x, logs=TRUE, ig1=NULL, ig2=NULL, clmn.lab=dimnames(x)[[2]], row.lab=dimnames(x)[[1]], clmn.off=NULL, row.off=NULL,...)
x |
matrix or data.frame containing the values to be plotted.
|
logs |
If logs=TRUE , then log values are used.
|
ig1 |
The columns of x for cases in group 1 (see Details)
|
ig2 |
The columns in group 2. By default, all the columns not in group 1. |
clmn.lab |
Labels for the columns in the array. |
row.lab |
Labels for the rows in the array. |
clmn.off |
Offset for printing the column labels (<0 to put labels outside the plot). |
row.off |
Offset for printing the row labels (<0 to put labels outside the plot). |
... |
Additional arguments to image and text (see par )
none
|
Values within a row are centered and normalized to have variance 1. If
ig1
is not given, then the values are centered to have mean 0.
If ig1
is given, the values are centered so the means of the columns in
ig1
and ig2
are equal in magnitude and opposite in direction. The
plot is
thus useful for comparing within rows, but differences in colors
between rows have no meaning.
A graphics device supporting image plots must be initialized prior to calling this function. Under Splus 3.4 for unix, the following command (without the line breaks) initializes the X window motif plot window to use 30 colors from blue (lowest levels) to yellow (highest levels) for the image plots (in this scheme a value half way between the lowest and highest values would be a medium intensity gray).
motif("-xrm 'sgraphMotif.colorSchemes : background : black; lines : yellow cyan magenta green MediumBlue red; text : white yellow cyan magenta green MediumBlue red; images : blue 30 yellow'")
An image plot is created on the current graphics device
plot.permax
set.seed(1292) ngenes <- 1000 m1 <- rnorm(ngenes,4,1) m2 <- rnorm(ngenes,4,1) exp1 <- cbind(matrix(exp(rnorm(ngenes*5,m1,1)),nrow=ngenes), matrix(exp(rnorm(ngenes*10,m2,1)),nrow=ngenes)) exp1[exp1<20] <- 20 sub <- exp1>20 & exp1<150 exp1[sub] <- ifelse(runif(length(sub[sub]))<.5,20,exp1[sub]) dimnames(exp1) <- list(paste('x',format(1:ngenes,justify='l'),sep=''), paste('sample',format(1:ncol(exp1),justify='l'),sep='')) dimnames(exp1) <- list(paste('x',1:ngenes,sep=''), paste('sample',1:ncol(exp1),sep='')) exp1 <- round(exp1) plot.expr(exp1[1:20,])