Question

ComplexHeatmap Scale by Row

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andrew.j.skelton73 ▴ 370

@andrewjskelton73-7074

Last seen 8 months ago

United Kingdom

Hi,

I'd like to scale by row, similar to a feature in heatmap.2 for the complexHeatmap package and wondered if there was a way anyone knows of?

Cheers

ComplexHeatmap heatmap • 10.0k views

ADD COMMENT • link updated 9.5 years ago by James W. MacDonald 67k • written 9.5 years ago by andrew.j.skelton73 ▴ 370

score 2 · Accepted Answer · 2015-06-03

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 14 hours ago

United States

Sure. Use the scale() function on your matrix, then feed it to Heatmap().

ADD COMMENT • link 9.5 years ago James W. MacDonald 67k

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Thanks for the simple answer!

ADD REPLY • link 9.5 years ago andrew.j.skelton73 ▴ 370

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Interestingly, when I went and took a look at the heatmap.2 code for scale by row, it's:

rm            <- rowMeans(x)
x             <- sweep(x, 1, rm)
sx            <- apply(x, 1, sd)
x             <- sweep(x, 1, sx, "/")

ADD REPLY • link 9.5 years ago andrew.j.skelton73 ▴ 370

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Right. The scale() function works on the columns, so you have to do some transposing.

> z <- matrix(rnorm(100),10)
> rm <- rowMeans(z)
> sx <- apply(z, 1, sd)
> zz <- sweep(z,1,rm)
> zz <- sweep(zz, 1, sx, "/")
> zzz <- t(scale(t(z)))
> all.equal(zz, zzz, check.attributes = FALSE)
[1] TRUE

ADD REPLY • link 9.5 years ago James W. MacDonald 67k