Hi,

I have a massive dataset that I want to use to make a heatmap using the Complexheatmap package. However, I'm getting the following error

Error: node stack overflow
Error during wrapup: node stack overflow

I am not at liberty to share my original dataset and hence here is a sample data.

new_df=data.frame("Spock2"=rep(0,10),"Col4a3"=c(rep(0,3),rep(2,2),rep(0,5)),"Syt1"=c(rep(0,8),rep(4,2)),"Pacrg"=c(rep(0,4),4,rep(0,2),rep(3,3)))

new_df=new_df[rep(seq_len(nrow(new_df)), each=300),]
Heatmap(as.matrix(new_df), row_labels = rep("",3000))

How do I fix this issue ? Any ideas ?

Thanks, Apoorva

I cannot solve this problem, but you can add small random values to the original matrix to make no duplicated rows:

m = as.matrix(new_df)
m = m + runif(length(m), min = 0, max = 1e-10)
Heatmap(m, show_row_names = FALSE)

To control the legend, set proper values in heatmap_legend_param argument.

https://jokergoo.github.io/ComplexHeatmap-reference/book/legends.html#heatmap-and-annotation-legends

Now I add a new argument jitter in Heatmap() which internally adds random shift to the original matrix. The matrix is only modified when making the dendrograms. The heatmap bodies and the legends are not affected:

m = as.matrix(new_df)
Heatmap(m, show_row_names = FALSE, jitter = TRUE)

or

m = as.matrix(new_df)
Heatmap(m, show_row_names = FALSE, jitter = 1e-10)

The random values are generated from the uniform distribution within (0, jitter) or (0, 1e-10).

Please update the package from GitHub:

library(devtools)
install_github("jokergoo/ComplexHeatmap")