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Editorial Team
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Asked: 2026-06-03T19:46:43+00:00

Here is data: set.seed(123) mat <- matrix(rnorm(5000, 0.5, 0.2), 50) heatmap (mat) mat[mat >

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Here is data: 

set.seed(123)
mat <- matrix(rnorm(5000, 0.5, 0.2), 50)
heatmap (mat)

enter image description here

mat[mat > 0.05] <- NA
heatmap (mat)

Error in hclustfun(distfun(x)) : 
  NA/NaN/Inf in foreign function call (arg 11)

By replacing with other values (arbitrary can help) but it can trick the readers as it will pick color from the same scale, which is not true. So I want to put completely different color for those value greater than 0.05. 

mat[mat > 0.05] <- 0.1
heatmap (mat)

enter image description here

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1 Answer

  1. Editorial Team

    maybe…

    library(gplots)
set.seed(123)
mat <- matrix(rnorm(5000, 0.5, 0.2), 50)
heatmap.2(mat, breaks=c(-1,0.02,0.05,1), col=c("yellow", "red", "blue"), 
# aiming for >0.05 is blue
dendrogram="both", trace="none")

    Basically play around with col= and breaks=

    looks like:

    enter image description here

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