Re: [R] heatmap

From: Nair, Murlidharan T <mnair_at_iusb.edu>
Date: Wed, 02 Jul 2008 16:14:21 -0400

I tried the following myself and I almost have something to work with. But I still need a little input.

#Plots a filled contour
# Can someone help me in increasing the resolution as my data range is 0-11? Also I need to put the row and column names on the axes. x <- 1:nrow(data)
y <- 1:ncol(data[,-1])
filled.contour(x, y, as.matrix(data[,-1]), color = terrain.colors,

    plot.title = title(main = "", xlab = "", ylab = ""),     key.title = title(main="Hex count"),     key.axes = axis(4,asp=1))# maybe also asp=1

#Plots the image directly.
#Can I specify specific set of colors in for the image to correspond to a particular value in the data matrix?
#I need to put the row and column names on the axes and make a key . Any help here please ?

image(x,y,as.matrix(data[,-1]),col=topo.colors(12)))

Thanks ../Murli



From: r-help-bounces_at_r-project.org [r-help-bounces_at_r-project.org] On Behalf Of Nair, Murlidharan T [mnair_at_iusb.edu] Sent: Wednesday, July 02, 2008 2:02 PM
To: r-help_at_r-project.org
Subject: [R] heatmap

I am interested in plotting a matrix of data using heatmap to reflect frequency of positional occurrence of certain strings. I am not interested in clustering them. I also want to make a key for the colors.Can someone help me with that. I am appending a portion of my data here. Thanks ../Murli

data<-dput(unique.data[1:20,1:20])
structure(list(A1 = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), A2 = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L ), A3 = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 1L,

0L, 0L, 0L, 0L, 0L, 0L, 0L), A4 = c(0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), A5 = c(0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L), A6 = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), A7 = c(0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L),

    A8 = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,

    0L, 0L, 0L, 0L, 0L, 0L, 0L), A9 = c(0L, 0L, 0L, 0L, 0L, 1L,
    0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L),
    A10 = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
    0L, 0L, 0L, 0L, 0L, 0L, 0L), A11 = c(0L, 0L, 0L, 0L, 0L,
    0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L
    ), A12 = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,     0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), A13 = c(0L, 0L, 0L, 0L,     0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,     0L), A14 = c(0L, 0L, 2L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L,
    0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), A15 = c(0L, 0L, 1L,
    0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L,
    0L, 0L), A16 = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
    0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 1L, 0L), A17 = c(0L, 0L,
    0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
    0L, 0L, 0L), A18 = c(0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L,
    0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), A19 = c(0L,
    0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
    0L, 0L, 0L, 0L), A20 = c(0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L,
    0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L)), .Names = c("A1",

"A2", "A3", "A4", "A5", "A6", "A7", "A8", "A9", "A10", "A11",
"A12", "A13", "A14", "A15", "A16", "A17", "A18", "A19", "A20"
), row.names = c("gggggg", "gttagg", "gggtgg", "ggtagg", "aggtag",

"ggggtg", "gtttag", "ggttag", "gggggt", "agttag", "tttagg", "aggggg",
"tggggg", "ggtggg", "gtaggt", "aggttt", "taggtt", "agtttg", "agttcg",
"taggta"), class = "data.frame")

heatmap(as.matrix(data))



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