Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent

Question

[luzglongoria]

Hi,

I am trying to create a heatmap.

Before I need to transform my dataset:

data <- heatmap_data
rnames <- data[,1]                            # assign labels in column 1 to "rnames"
mat_data <- data.matrix(data[,2:ncol(data)])  # transform columns (I have) into a matrix
rownames(mat_data) <- rnames                  # assign row names

But when I run the last one I get this error message:

   Error in dimnames(x) <- dn : 
  length of 'dimnames' [1] not equal to array extent

If I do:

head(data)
ID                          s21   s22   s23   s24   s25   s31   s32   s33   s34   s35
  <chr>                     <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 TRINITY_DN34816_c1_g1_i2  0.233 0     1.31  0.127 0.822 2.06  1.44  0.749 1.79  2.61 
2 TRINITY_DN10000_c0_g1_i1  3.01  1.78  1.38  0.798 0.855 3.18  2.99  3.54  3.05  1.20
3 TRINITY_DN100041_c0_g1_i1 3.66  2.80  2.14  1.21  1.26  3.83  3.85  4.27  3.76  1.98 
4 TRINITY_DN100086_c0_g1_i1 0.556 0.438 0.176 0.145 0.03  0.533 0.511 0.524 0.344 0.134
5 TRINITY_DN19297_c0_g1_i1  0.559 0.23  0.224 0.11  0.024 1.12  1.08  2.08  2.05  0.56 
6 TRINITY_DN133973_c0_g1    0     0.275 0     0     0     2.48  0.964 2.18  0.8   1.34

and

head(mat_data)
   s21   s22   s23   s24   s25   s31   s32   s33   s34   s35
[1,] 0.233 0.000 1.309 0.127 0.822 2.062 1.435 0.749 1.788 2.610
[3,] 3.664 2.799 2.137 1.207 1.258 3.828 3.849 4.269 3.760 1.984
[4,] 0.556 0.438 0.176 0.145 0.030 0.533 0.511 0.524 0.344 0.134
[5,] 0.559 0.230 0.224 0.110 0.024 1.118 1.085 2.084 2.046 0.560
[6,] 0.000 0.275 0.000 0.000 0.000 2.477 0.964 2.176 0.800 1.340

How can I solve this problem?

[zx8754]

Make your problem reproducible, your code works fine with below example dataframe:

# example dataframe
set.seed(1); data <- data.frame(x = LETTERS[1:2], y = runif(2),  z = runif(2), stringsAsFactors = FALSE)
# data
#   x         y         z
# 1 A 0.2655087 0.5728534
# 2 B 0.3721239 0.9082078

rnames <- data[, 1]
# rnames
# [1] "A" "B"

mat_data <- data.matrix(data[,2:ncol(data)])
#              y         z
# [1,] 0.2655087 0.5728534
# [2,] 0.3721239 0.9082078

rownames(mat_data) <- rnames 
# mat_data
#           y         z
# A 0.2655087 0.5728534
# B 0.3721239 0.9082078

Answer 1

[luzglongoria]

Solved!

It was a problem with the title of the first column :)

[Friederike]

yes, rnames <- data[,1] will extract the content of the first column, not the first row. That would be achieved with rnames <- data[1,].

[Madhuri Haque]

Hello,

Could you please elaborate a little bit about how to fix this issue with the title of the first column. I am stuck with this issue for the last couple of days!

[Kaz]

Hi, I'm not really sure what is meant with "problem with the title of the first column", but you could run rnames <- data$X1 where X1 is the title of the first column (if your first column name (row 1, column 1) is empty R will call it X1), instead of rnames <- data[,1]. This will give rnames right object form for next step.

Answer 2

[Abdul Aziz]

The reason for the error is because the data was not classified as data.frame I solved this by adding a new line in the syntax.

    data <- heatmap_data
    data<-as.data.frame(data) # New line added
    rnames <- data[,1]                            # assign labels in column 1 to "rnames"
    mat_data <- data.matrix(data[,2:ncol(data)])  # transform columns (I have) into a matrix
    rownames(mat_data) <- rnames                  # assign row names