hide the NA values when using display_numbers function in pheatmap

Question

I am plotting heatmap by pheatmap package in r.

I applied the display_numbers function to display the values in a matrix into the heatmap, and I got:

I got so many NA in my matrix and I would like to hide them in the heatmap, how can I do that?

Hi @leeleelee please consider editing your question to include sample code, sample data and expected output. You could use `dput(head(mysampledata,20))` to add sample data to your question. — NelsonGon, Dec 25 '18 at 14:25

score 2 · Accepted Answer · answered Dec 25 '18 at 14:32

First off, it is a lot easier for people to help you if you were to provide reproducible and minimal sample data. Please consider reviewing how to provide a minimal reproducible example/attempt for future posts.

As to your question:

Let's generate some sampe data
```
set.seed(2018)
mat <- matrix(runif(20), 4, 5)
```
We use a second matrix to display values via the argument display_numbers of pheatmap. Here we simply copy the original matrix and randomly generate some NA values:
```
mat2 <- mat
mat2[mat2 < 0.5] <- NA
```
We now replace NA values with empty strings.
```
mat2[is.na(mat2)] <- ""
```
Let's show the heatmap
```
pheatmap(mat, display_numbers = mat2)
```

Thanks for all the advice, I will do my best to ask a good question next time. — , Dec 26 '18 at 00:50

hide the NA values when using display_numbers function in pheatmap

1 Answers1