Using a pheatmap in arrangeGrob

Question

I'm attempting to plate two plots in the same .jpg using arrangeGrob(). I've only just started learning about grids and grobs and I think I know what the problem is: pheatmap is a grid object and containing grob objects, not allowing me to put it in arrangeGrob. Is this true?

Would I somehow need to put the qplot in a grid and the pheatmap in a grid and then put those grids in a new grid?

library(grid)
library(gridExtra)
library(pheatmap)
library(ggplot2)
hmdat=rbind(c(1,2,3),
            c(3,4,5),
            c(5,6,7))
hm=pheatmap(hmdat)
qp=qplot(1,1)
lm=rbind(c(1,2,2),
         c(1,2,2))
jpeg("plots.jpg")
arrangeGrob(qp,hm, layout_matrix=lm)
dev.off()

The above code snippet runs just fine when using

arrangeGrob(qp,qp, layout_matrix=lm)

Gon

Try arrangeGrob(qp, hm[[4]], layout_matrix=lm). The manual page for pheatmap() clearly states in the Values section that it returns a list of components, but it fails to mention component #4, which is the gtable of the plot. You have to index it specifically since it's not going to trigger R's print method lookup/execution for that object inside the function call. – Augment

That works perfectly, thanks! Any suggestion as to how I can find the solution for myself when I face this kind of problem again? Or is list value 4 being the gtable just a thing you have to somehow know? If you enter your solution as the answer, I will set the question to answered. – Gon

Answer 1

I'm not sure if you wanted to have 6 figures or you wanted to have two figures one with twice as wide as the other one (I tried to do minimum code change):

library("grid")
library("gridExtra")
library("pheatmap")
library("ggplot2")

hmdat=rbind(c(1,2,3),
            c(3,4,5),
            c(5,6,7))

hm <- pheatmap::pheatmap(hmdat)
qp <- qplot(1,1)

lm <- rbind(c(1,2,2),
         c(1,2,2))
grid.arrange(grobs = list(qp,hm[[4]]), layout_matrix = lm)

which will give you:

The same way you can have multiple pheatmaps side-by-side:

library("grid")
library("gridExtra")
library("pheatmap")

hmdat <- rbind(c(1,2,3),
            c(3,4,5),
            c(5,6,7))

hm <- pheatmap::pheatmap(hmdat)

lm <- rbind(c(1,2),
         c(3,3))
grid.arrange(grobs = list(hm[[4]],
                          hm[[4]],
                          hm[[4]]),
             layout_matrix = lm)

As @hrbrmstr mentioned in the comment, you should use the 4th item in the pheatmap object. Also remember to provide grobs as list to the grid.arrange

Theurich

Getting this error this S4 class is not subsettable – Fou

@hirak-sarkar I just tried it with R version 4.1.0, pheatmap_1.0.12 and gridExtra_2.3 and it worked just fine. Also I double checked the str(hm) and is.list(hm) and confirmed that the object is in fact S3. I don't know where you got the S4 ! Please double check your versions and objects. – Theurich

Ok I figured, there are two pheatmap-s in my session pheatmap::pheatmap is the correct one. There was also another from ComplexHeatmap. – Fou