[R] heatmap.3

[joonR]

Hello again,
lately I have been playing a lot with heatmap functions,
in particular I complemented heatmap.2 with a nice feature from
heatmap.plus,
i.e. the possibility of assigning a matrix to ColSideColors so to take into
account more annotations.
Below is the code I introduced in heatmap.2, everything else is maintained
equal to heatmap.2:

  
     if (!missing(ColSideColors)) {
       #if (!is.matrix(ColSideColors)) 
       #stop("'ColSideColors' must be a matrix")
        if (!is.character(ColSideColors) || dim(ColSideColors)[1] != 
            nc) 
            stop("'ColSideColors' dim()[2] must be of length ncol(x)")
        lmat <- rbind(lmat[1, ] + 1, c(NA, 1), lmat[2, ] + 1)
        lhei <- c(lhei[1], 0.2, lhei[2])
    }
        if (!missing(RowSideColors)) {
       #if (!is.matrix(RowSideColors)) 
       #stop("'RowSideColors' must be a matrix")
        if (!is.character(RowSideColors) || dim(RowSideColors)[1] != 
            nr) 
            stop("'RowSideColors' must be a character vector of length
nrow(x)")
        lmat <- cbind(lmat[, 1] + 1, c(rep(NA, nrow(lmat) - 1), 
            1), lmat[, 2] + 1)
        lwid <- c(lwid[1], 0.2, lwid[2])
    }
        
    
    
    lmat[is.na(lmat)] <- 0
    
    }
        
    if (length(lhei) != nrow(lmat)) 
        stop("lhei must have length = nrow(lmat) = ", nrow(lmat))
    if (length(lwid) != ncol(lmat)) 
        stop("lwid must have length = ncol(lmat) =", ncol(lmat))
    op <- par(no.readonly = TRUE)
    on.exit(par(op))
    layout(lmat, widths = lwid, heights = lhei, respect = FALSE)
    
    if (!missing(RowSideColors)) {
	if (!is.matrix(RowSideColors)){
       		par(mar = c(margins[1], 0, 0, 0.5))
        	image(rbind(1:nr), col = RowSideColors[rowInd], axes = FALSE)
        } 
        else{
        par(mar = c(margins[1], 0, 0, 0.5))
        rsc = RowSideColors[rowInd, ]
        rsc.colors = matrix()
        rsc.names = names(table(rsc))
        rsc.i = 1
        for (rsc.name in rsc.names) {
            rsc.colors[rsc.i] = rsc.name
            rsc[rsc == rsc.name] = rsc.i
            rsc.i = rsc.i + 1
        }
        rsc = matrix(as.numeric(rsc), nrow = dim(rsc)[1])
        image(t(rsc), col = as.vector(rsc.colors), axes = FALSE)
        if (length(colnames(RowSideColors)) > 0) {
            axis(1, 0:(dim(rsc)[2] - 1)/(dim(rsc)[2] - 1),
colnames(RowSideColors), 
                las = 2, tick = FALSE)
                }
        }
    }
    if (!missing(ColSideColors)) {
        if (!is.matrix(ColSideColors)){
        	par(mar = c(0.5, 0, 0, margins[2]))
        	image(cbind(1:nc), col = ColSideColors[colInd], axes = FALSE)
        }
        else{    
    	par(mar = c(0.5, 0, 0, margins[2]))
        csc = ColSideColors[colInd, ]
        csc.colors = matrix()
        csc.names = names(table(csc))
        csc.i = 1
        for (csc.name in csc.names) {
            csc.colors[csc.i] = csc.name
            csc[csc == csc.name] = csc.i
            csc.i = csc.i + 1
        }
        csc = matrix(as.numeric(csc), nrow = dim(csc)[1])
        image(csc, col = as.vector(csc.colors), axes = FALSE)
        if (length(colnames(ColSideColors)) > 0) {
            axis(2, 0:(dim(csc)[2] - 1)/(dim(csc)[2] - 1),
colnames(ColSideColors), 
                las = 2, tick = FALSE)
                }
        }
    }
    
What is weird is the fact that the dimension of histogram plotted above the
heatmap, accounting for the annotations, is always the same (fixed!), so
when you have 3 or more annotations, the same length of the bars is divided
by 3 or more, making the reading of the figure impossibile..

Does anyone know how to fix this? Thanks!

g

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