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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