Heatmap error: 'x' must be a numeric matrix

Question

[adnan.sabar7865]

Hi everyone

I'm making heatmap by using r studio. My data have 4 rows, 1 with name and 3 with values. I export excel sheet by selecting numeric.

library(readxl)
drug_class <- read_excel("C:/Users/hondalab/OneDrive/Desktop/16s NTR/Hiseq/drug_class.xlsx", 
    col_types = c("text", "numeric", "numeric", 
        "numeric"))

When I put heatmap command but I got this error.

heatmap(drug_class)
Error in heatmap(drug_class) : 'x' must be a numeric matrix

print command showed this;

> print(drug_class)
# A tibble: 29 x 4
   `drug class`                   `NTR 1 Rain` `NTR 2 Dry` `NTR 2 Rain`
   <chr>                                 <dbl>       <dbl>        <dbl>
 1 aminocoumarin                       0.00233    0.0239      0.00393  
 2 aminoglycoside                      0.00559    0.136       0.0725   
 3 antibacterial free fatty acids      0          0           0.0000264
 4 benzalkonium chloride               0          0.000615    0.000123 
 5 carbapenem                          0.00255    0.0321      0.0184   
 6 cephalosporin                       0.00444    0.0644      0.0485   
 7 cephamycin                          0.00240    0.0264      0.00830  
 8 diaminopyrimidine                   0.00244    0.0324      0.0412   
 9 fluoroquinolone                     0.00637    0.0528      0.0317   
10 fosfomycin                          0          0           0.000412 
# ... with 19 more rows

Can anybody help to solve this error. Thanks!

[kashiff007]

Your first column is numeric and you need to convert it as row names or you can also skip this.

col_types <- as.matrix(col_types[,2:4])

[adnan.sabar7865]

after converting this, it' still showing same error.

[zx8754]

Related SO post:

• Heatmap error with : 'x' must be a numeric matrix

Answer 1

[rpolicastro]

heatmap says it requires a numeric matrix, so you probably have to convert your tibble to a matrix.

drug_class <- as.data.frame(drug_class)
rownames(drug_class) <- drug_class[, 1]
drug_class[, 1] <- NULL
drug_class <- as.matrix(drug_class)

Tidyverse ansywer

library("tidyverse")

drug class <- drug_class %>%
  column_to_rownames("drug class") %>%
  as.matrix

[adnan.sabar7865]

Thanks. it works.

Answer 2

[cpad0112]

can you try following?

heatmap(as.matrix(drug_class[,2:ncol(drug_class)]))

you can also try:

library(data.table)
heatmap(as.matrix(as.data.table(iris),rownames = 1))

Instead of default heatmap, I would suggest pheatmap and complexheatmap packages.