Dear all
I have a simple question about R drawing heatmap. I produced a heatmap using the following code, however, I want to swap the colors between yellow and red (i.e., by default yellow represent high value while red represent low values, i want to swap them).
My second question is: how to add white lines for the boundaries of each unit ? THANKS a lot!
n1 <- read.table(file="test.txt", header=T)
n1 <- data.matrix(n1)
heatmap.2(n1, trace="none",col=heat.colors(256))
Try this
n1 <- read.table(file="test.txt", header=T)
n1 <- data.matrix(n1)
col = heat.colors(256)
col = col[order(col,decreasing=T)]
heatmap.2(n1, trace="none",col=col)
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written
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arno.guille
Hi Irsan and arno.guille, your comments are very helpful,but I still have problem: the picture color becomes white and red! I want it to be between yellow and red.
Sorry for my second unclear question. Each value is presented by a color cell in R heatmap, but by default the cell does not have boundary lines. I want to add white (or gray) boundary lines, and ideally I can adjust the width of the boundary line. THANKS a lot!
With the function colorRampPalette you can create your own gradient color.
For example:
col=colorRampPalette(c("yellow","red"))
col(100)
For the second question, I don't think it's possible to do it with R
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written
by
arno.guille
You can't create the boundary lines with R, but you can use the rowsep or colsep to create white/grey lines between the cells.
This is just a vector of numeric values, which says how width the gap between two columns or rows should be.
# block sepration
colsep,
rowsep,
sepcolor="white",
sepwidth=c(0.05,0.05),
colsep, rowsep, sepcolor
(optional) vector of integers indicating which columns or rows should be separated from the preceding columns or rows by a narrow space of color `sepcolor`.
sepwidth
(optional) Vector of length 2 giving the width (colsep) or height (rowsep) the separator box drawn by colsep and rowsep as a function of the width (colsep) or height (rowsep) of a cell. Defaults to c(0.05, 0.05)
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I don't understand your second question but for your first question simply use
If you are using heatmap.2, then I think you use rowsep and/or colsep to draw lines between the entries in the body of the heatmap