Looping over matrices

Question

thx for your help!

I have 2 matrices: Mx1 and Mx2 And I would like to make heatmaps using pheatmap by looping on selected matrices in the R environment

I tried:

Matrices_list <- c(Mx1, Mx2)
for( i in Matrices_list_list ){pheatmap(i, filename= "i.pdf")}

but obviously doesn't works The problems is that the Df_list now is a merge of both Mx instead of 2 distinct datasets in which I cant loop. Its looping in each element of the combined Df_list

Desired output:

pheatmap(Mx1, filename="Mx1.pdf")
pheatmap(Mx2, filename="Mx2.pdf")

Thx again for your help :)

Answer 1

A matrix is a vector with dimension attributes (usually 2D). The use of c function on two matrices, removes the dimension attributes and return a single 1 dimensional vector with length equal to the length(Mx1) + length(Mx2).

As showed in the comments, if we need to keep the matrix as itself store it in a list with names attribute as the object names of the individual matrices. With dplyr::lst, by default it generates the names of the list as object names

library(dplyr)
Matrices_list <- lst(Mx1, Mx2)

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Regarding the for loop used in OP's post

for(i in Matrices_list ){...

the i is the individual matrix element, which doesn't have any names attribute. This can be otherwise described as a for each loop i.e. for each element 'x' of 'Matrices_list'. In other languages such as C++, the for each syntax would be

for(auto i : Matrices_list) {...

Instead of looping over the object elements, loop over the sequence

for(i in seq_along(Matrices_list)) {...

or the names attribute, extract those elements and the corresponding names to construct the file name.

---

With tidyverse, we can use imap or iwalk with .x the matrix element and .y the names of the list or the index (if the names are absent)

library(purrr)
library(stringr)
imap(Matrices_list, ~ pheatmap(.x, filename = str_c(.y, ".pdf")))
iwalk(Matrices_list, ~ pheatmap(.x, filename = str_c(.y, ".pdf")))

The difference in imap/iwalk is that iwalk doesn't print the return value on the console.