creating iterative named lists, with variable names including with operators

Question

SOLVED

pheno_vector = c("PAX5+PDL1-", "CD3+CD8+PD1-", "CD3+CD8-PD1+")
n = length(pheno_vector)
for (i in 1:(n-1)){
  for (j in (i+1):n){
    pheno1 = pheno_vector[i]
    pheno2 = pheno_vector[j]
    pairs = list(c(pheno1, pheno2))

    colors = c("cyan", "magenta")
    names(colors) = c(pheno1,pheno2)
    print(colors)

produces

               PAX5+PDL1- CD3+CD8+PD1- 
                "cyan"    "magenta" 
               PAX5+PDL1- CD3+CD8-PD1+ 
                "cyan"    "magenta" 
             CD3+CD8+PD1- CD3+CD8-PD1+ 
                "cyan"    "magenta"

I have a problem with creating a named list, in which the names should be able to iteratively change, but should be pasted for visual plotting.

I am working with data from Vectra Imaging, involving phenotypes of cells.

As there are multiple phenotypes, i want to iteratively make pairs of phenotypes to visually make plots as shown in the example in https://rdrr.io/github/PerkinElmer/phenoptr/man/spatial_distribution_report.html

Currently my code adapted to my data looks like this

pheno1 = "PAX5+PDL1-"
pheno2 = "CD3+CD8+PD1-"
pairs = list(c("PAX5+PDL1-", "CD3+CD8+PD1-"))
colors = c('PAX5+PDL1-'="cyan", 'CD3+CD8+PD1-'="magenta")
colors

This returns

>  PAX5+PDL1- CD3+CD8+PD1- 
>     "cyan"    "magenta"

The pairs and colors is used to make the plots. Now I want to iteratively make plots for more pairs of phenotypes that I have in the data. In the end I'd like to for-loop over pheno1 and for-loop over pheno2 obtained from a general phenotypes-vector pheno_vector which contains .

What I tried is

pheno1 = "PAX5+PDL1-"
pheno2 = "CD3+CD8+PD1-"
pairs = list(c(pheno1, pheno2))
colors = c(pheno1="cyan", pheno2="magenta")
colors

Which returns

>     pheno1     pheno2 
>     "cyan"    "magenta"

I understand why I see pheno1 and pheno2, and not "PAX5+PDL1-" and "CD3+CD8+PD1-". I tried some paste and eval methods as in Create a variable name with "paste" in R? but that did not work out.

Assign("PAX5+PDL1-", "cyan")

does not work out as I don't know how to make it into a named list then.

In the end I'd like to have this as a result

pheno_vector = c("PAX5+PDL1-", "CD3+CD8+PD1-", "CD3+CD8-PD1+")
for (pheno1 in pheno_vector){
 for (pheno2 in pheno_vector){
  if (uniqueness_statement and permutation_statement){
     pairs = list(c(pheno1, pheno2))
     colors = c(pheno1="cyan", pheno2="magenta")
     colors

Which should return

>     PAX5+PDL1-     CD3+CD8+PD1- 
>     "cyan"             "magenta" 
>     PAX5+PDL1-     CD3+CD8-PD1+ 
>     "cyan"              "magenta" 
>     CD3+CD8+PD1-   CD3+CD8-PD1+
>     "cyan"           "magenta"

So these are specifically named lists, which they need to be for later plotting.

Doe anyone have a solution for this?

Simon · Accepted Answer · 2019-05-14T13:47:22.377

You could name the colors-vector once it is created:

library(gtools)

pheno_perms <- permutations(length(pheno_vector), 2, pheno_vector)
combs <- apply(apply(pheno_perms, 1, sort), 2, paste0, collapse=' ')
pheno_perms <- pheno_perms[match(unique(combs), combs), ]

for (i in 1:nrow(pheno_perms)){
  pheno1 <- pheno_perms[i, 1]
  pheno2 <- pheno_perms[i, 2]
  pairs = list(c(pheno1, pheno2))
  colors = c("cyan", "magenta")
  names(colors) <- c(pheno1, pheno2)
  print(colors)
}

This produces:

CD3+CD8-PD1+ CD3+CD8+PD1- 
      "cyan"    "magenta" 
CD3+CD8-PD1+   PAX5+PDL1- 
      "cyan"    "magenta" 
CD3+CD8+PD1-   PAX5+PDL1- 
      "cyan"    "magenta"

P.S.: I hope I interpret correctly what you mean by uniqueness_statement and permutation_statement!

Thank you for your response. Seems that I got the syntax of names(colors) wrong. It is fixed now, see my edit. The permutation and uniqueness statement were not from importance but wanted to give an indication why the output had 3 elements. — Bo5man, May 15 '19 at 09:13

creating iterative named lists, with variable names including with operators

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