CODEWITHSUNDEEP
r
ThePooh
ThePooh

Reputation: 101

Set sepwidth heatmap.2 (gplots)

I am trying to increase sepwidth betweeen rows and columns in my heatmap. I use sepwidth, however when i try to increase sepwidth, it does not move columns or rows to right.

Here is an example

library(gplots)
mat = matrix( rnorm(100), ncol=5 )
colorside = gray(1:5/5)
bk1 = seq(min(mat),max(mat),length.out=11)
col = redgreen(10)

# And now the heatmap
heatmap.2( mat, 
           key=FALSE, 
           trace="none",
           ColSideColors=colorside,
           cexRow=0.6,
           breaks=bk1,
           col=col,
           sepwidth=c(0.4,0.4),
           sepcolor="purple",
           colsep=1:ncol(mat),
           rowsep=1:nrow(mat))

Thank you for any help.

Upvotes: 2

Views: 1029

Answers (1)

KoenV
KoenV

Reputation: 4283

I am not sure I completely understand what you want. Anyway my guess is that you want to add space before the first column and above the first row.

sepwidth defines the amount of space between columns and rows, and applies that space based on the values in the vectors colsep and rowsep. In your case, you simple have to start one unit earlier in the definitions of colsep and rowsep, like in the following code:

setseed(8765) ## added for reproducibility

# Your code
library(gplots)
mat = matrix( rnorm(100), ncol=5 )
colorside = gray(1:5/5)
bk1 = seq(min(mat),max(mat),length.out=11)
col = redgreen(10)

## First call to get "hm1"
hm1 <- heatmap.2( mat, 
                 key=FALSE, 
                 trace="none",
                 ColSideColors=colorside,
                 cexRow=0.6,
                 breaks=bk1,
                 col=col,
                 sepwidth=c(0.4,0.4),
                 sepcolor="purple",
                 colsep=0:ncol(mat), ## changed
                 rowsep=0:nrow(mat)) ## changed

# Look at lwid and define a new one to use
hm1$layout$lwid
# [1] 1.5 4.0
my_lwid <- c(1.0, 4.5)

## call with altered lwid
hm2 <- heatmap.2( mat, 
                  key=FALSE, 
                  trace="none",
                  ColSideColors=colorside,
                  cexRow=0.6,
                  breaks=bk1,
                  col=col,
                  sepwidth=c(0.4,0.4),
                  sepcolor="purple",
                  lwid = my_lwid,     ## added
                  colsep=0:ncol(mat),
                  rowsep=0:nrow(mat)) 
hm2$layout$lwid

Please, let me know whether this is what you wanted.

Upvotes: 3

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