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how to display multiple row annotations on pheatmap

I am interested in adding multiple row annotations to my heatmap using the pheatmap function in R (example: https://stackoverflow.com/questions/41628450/r-pheatmap-change-annotation-colors-and-prevent-graphics-window-from-popping-up). The examples I see online all give only one annotation. What is the easy way to extend it to multiple row annotations?

pheatmap
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written by lavanya.kannan • lavanya.kannan

If you hablve a data frame or matrix with your gene names annotated for each category. Then you can easily parse it in pheatmap as annotation_row= . Check the pheatmap tutorial. Alternatively if it's on the fly then you have to create vectors of the category with your gene names or rownames that you intend to project and create a data frame with them. Once done while you write code for the pheatmap just parse that data frame in to the row annotate handler. It should work.

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written by ivivek_ngs ivivek_ngs

I have a data frame for the annotation, and I tried doing it, as you've mentioned. For some reason, I always get this error: Error in cut.default(a, breaks = 100) : 'x' must be numeric. Could you help me understand what this error means?

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written by simranv96 • simranv96

I would encourage you to search the error in this forum or Google or StackOverflow. In case you do not find it. Please write a new post in those mentioned forums detailing your problem scope, code snippet, and error, so that we can better assist.

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written by ivivek_ngs ivivek_ngs

Thanks for the comments; I made it to work for categorial variables. Now I am trying to add row annotations for categorial variables. In otherwords I am trying to add a heatmap on continuous variables as row annotations for another heatmap. Do I have to to define the bin sizes and treat the continuous variables as categorial variables, or is there a easier way to get around this step?

Thanks, Lavanya

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written by lavanya.kannan • lavanya.kannan

you can use the continuous annotations as is, pheatmap will take care of it

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written by Friederike Friederike

1 answer

from the pheatmap help:

# make test matrix
test = matrix(rnorm(200), 20, 10)
test[1:10, seq(1, 10, 2)] = test[1:10, seq(1, 10, 2)] + 3
test[11:20, seq(2, 10, 2)] = test[11:20, seq(2, 10, 2)] + 2
test[15:20, seq(2, 10, 2)] = test[15:20, seq(2, 10, 2)] + 4
colnames(test) = paste("Test", 1:10, sep = "")
rownames(test) = paste("Gene", 1:20, sep = "")

# define the annotation
annotation_row = data.frame(
                    GeneClass = factor(rep(c("Path1", "Path2", "Path3"), c(10, 4, 6))),
                  AdditionalAnnotation = c(rep("random1", 10), rep("random2", 10))
                )
rownames(annotation_row) = paste("Gene", 1:20, sep = "")

pheatmap(test, annotation_row = annotation_row)
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written by Friederike Friederike

This is a correct answer. Why has it not bee selected so?

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written by ajay nair • ajay nair

Indeed it is correct, and here is the proof: d

We are volunteers here and it is very difficult to keep track of activity in each and every thread. Apart from vacation/holidays, Biostars typically receives >1000 user visits per hour, throughout the entire day.

I have marked the answer as accepted myself.

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written by Kevin Blighe Kevin Blighe

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