Looping over a list of lists-CodePudding

I have the following code:

condition_1_top_genes = list("abc", "def", "efg")
condition_2_top_genes = list("a35", "2353", "rea3")
condition_3_top_genes = list("fae", "wai", "wtes")

top_genes = list(condition_1_top_genes, 
                 condition_2_top_genes,
                 condition_3_top_genes)

genotypes <- list("genotype1" = genotype1, 
                  "genotype2" = genotype2,
                  "genotype3"  genotype3)

for (i in length(genotypes)){
  for (j in ????){
    FeaturePlot(genotypes[[i]], features = ??)
  }
}

genotypes is a list of Seurat objects.

In the outer loop I'm looping over the Seurat objects, for the inner loop I want to loop over each of the lists in top_genes. So when i = 1 I want j to move along condition_1_top_genes, then when i=2, I want j to move along condition_2_top_genes, etc.

Any help on this syntax would be appreciated.

CodePudding user response：

[, wouldn't extract the list element, we need [[ to go inside the list and extract as vector. Also, we can use a single for loop instead of nested as top_genes showed is not a nested list but a list of vectors

for(i in seq_along(top_genes)) {
     top_genes[[i]] <- seq_along(top_genes[[i]]) * 3
}

CodePudding user response：

condition_1_top_genes = list("abc", "def", "efg")
condition_2_top_genes = list("a35", "2353", "rea3")
condition_3_top_genes = list("fae", "wai", "wtes")

top_genes = list(condition_1_top_genes, 
                condition_2_top_genes,
                condition_3_top_genes)

If I understand you correctly, you'd probably want to change the way you define the list top_genes.

# Define genes in character vector, allowing you to use concise syntax later on
condition_1_top_genes = c("abc", "def", "efg")
condition_2_top_genes = c("a35", "2353", "rea3")
condition_3_top_genes = c("fae", "wai", "wtes")

# Define list elements with names
top_genes = list(
  condition_1_top_genes = condition_1_top_genes, 
  condition_2_top_genes = condition_2_top_genes,
  condition_3_top_genes = condition_3_top_genes
)

Now you top_genes is a named list, you can access list elements in top_genes with [[""]] operator.

> top_genes[["condition_1_top_genes"]]
[1] "abc" "def" "efg"

# with paste0 function, you can access arbitrary list element
> i=1
> top_genes[[paste0("condition_",i,"_top_genes")]]
[1] "abc" "def" "efg"

# To access jth gene in condition_1_top_genes
> j=1
> top_genes[[paste0("condition_",i,"_top_genes")]][j]
[1] "abc"

So in your for loop, you can do:

for (i in length(genotypes)){
  for (j in length(top_genes[[paste0("condition_",i,"_top_genes")]])){
    FeaturePlot(genotypes[[i]], features = top_genes[[paste0("condition_",i,"_top_genes")]][j])
  }
}