[R] how to use vector of values to change row order of a heatmap

[PIKAL Petr]

Hi

Heatmap does not work with data frames (at least the version I have)

> b=as.data.frame(matrix(c(3,4,5,8,9,10,13,14,15,27,19,20),3,4))
> heatmap(b)
Error in heatmap(b) : 'x' must be a numeric matrix

With matrix, heatmap works as expected.

> b=matrix(c(3,4,5,8,9,10,13,14,15,27,19,20),3,4)
> heatmap(b)

However for row ordering you need to read Details of help page.

compare

> heatmap(b, Rowv=c(3,2,1))

with

> heatmap(b, Rowv=c(10,2,1))

If either is a vector (of ‘weights’) then the appropriate dendrogram is reordered according to the supplied values subject to the constraints imposed by the dendrogram, by reorder(dd, Rowv), in the row case. If either is
                                    ^^^^^^^^^
missing, as by default, then the ordering of the corresponding dendrogram is by the mean value of the rows/columns, i.e., in the case of rows, Rowv <- rowMeans(x, na.rm = na.rm). If either is NA, no reordering will be done for the corresponding side.

Cheers
Petr



> -----Original Message-----
> From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Fix Ace via
> R-help
> Sent: Monday, November 21, 2016 9:14 PM
> To: r-help at r-project.org
> Subject: [R] how to use vector of values to change row order of a heatmap
>
> Hello, there,
> R document for heatmap says that Rowv could be a vector of values to
> specify the row order. However, I couldn't figure out how to apply it. A
> simple example here:>
> b=as.data.frame(matrix(c(3,4,5,8,9,10,13,14,15,27,19,20),3,4))
> > b
>   V1 V2 V3 V4
> 1  3  8 13 27
> 2  4  9 14 19
> 3  5 10 15 20
> > row.names(b)=c("a","b","c")
> > b
>   V1 V2 V3 V4
> a  3  8 13 27
> b  4  9 14 19
> c  5 10 15 20
> > heatmap(as.matrix(b))
> What I got: "a" stays at the bottom of the heatmap.
>  Now I would like to put row "a" to the top row, how do I do that?I tried
> provide a vector of values (all the possible combination of 1,2,3) to Rowv,  "a"
> is always stay at the bottom Any input would be very helpful!
> Thanks.
> Ace
>
>       [[alternative HTML version deleted]]
>
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