Ah, I see it now. I had ignored the numbers before, I now formatted them in your original post so that it's a bit more obvious what you're actually asking. Your code does what it should; you may not like the consequences, but that's a different issue.
Using the pheatmap:::scale_rows function may illuminate what's going on:
## this is what the function does
> pheatmap:::scale_rows
function (x)
{
m = apply(x, 1, mean, na.rm = T)
s = apply(x, 1, sd, na.rm = T)
return((x - m)/s)
}
## and this is the result
> matrix(c(1.483681, 1.472528, 1.4296474), ncol = 3) %>% pheatmap:::scale_rows()
[,1] [,2] [,3]
[1,] 0.7616927 0.3707308 -1.132423
## which is the same as your code
> matrix(c(1.483681, 1.472528, 1.4296474), ncol = 3) %>% t %>% scale %>% t
[,1] [,2] [,3]
[1,] 0.7616927 0.3707308 -1.132423
As explained e.g. in wikipedia, the z-score is calculated by subtracting the (column or row mean) from the given value and dividing that by the standard deviation.
The mean of your 3 example values is 1.46, the sd is 0.029, so do the math yourself and you can see that the code is doing what it's supposed to be doing.
It might be easier for us to assist you if you posted the example images and the corresponding code. For example, it is not clear if you want to scale columns or rows or both.
Here is the code for scaled heatmap
![enter image description here][1]
And unscaled
![enter image description here][2]
Thanks.
And what exactly is the detail you don't like about the z-score? Which values do you think should be "the same"?
From what I can tell, your code does what you instructed it to do -- you're z-score-transforming the rows of your matrix, i.e. instead of displaying the actual values of
data, you're coloring the heatmap based on the distance of each entry to its row's mean.Btw, I would strongly recommend to not create an object named "type" because that's also the name of a base R function.
I got some values changed after scaling like this.
after scaling
Peaks like this not are not changed across the samples but after scaling, it showed differences.
I expected there should be some common regions (similar or same values) across my samples showing as the same color in a cluster.
Check out the formula below. The z-score is going to drastically reduce the influence of the dynamic range differences between individual rows, therefore small differences in a row with overall small values may get similar z-scores as differences that seem larger to you just because the numbers that are compared to each other live on a different scale. But relatively speaking, the differences from the mean may not be as dramatic (or similarly dramatic in the low-value-ranges).
Hello sophialovechan,
You have added multiple images improperly, hence they show up as links and not as embedded images. Please see How to add images to a Biostars post to add your images properly. You need the direct link to the image, not the link to the webpage that has the image embedded (which is what you have used here).
I will make the necessary changes for now.