How to make a loop function output its result as a data frame in R

Question

I created a function clique_function that selects variables from two data frames object_list and clique_list based on conditions and returns a new data frame from that clique_object.

Input:

clique_list is a list of cliques (groups of three nodes in a network) where each column represents a clique with three nodes composing it.

clique_list <- structure(c("ND1", "IS1", "IS3", "IS1", "IS3", "IS2", "ND2", "ND1", "IS1"), .Dim = c(3L, 3L))

object_list is a matrix with the nodes as rows and the occurrence of different object types as column.

object_list <- structure(list(CA1 = c(0.159159159159159, 0.222222222222222, 0.25, 0.115384615384615, 0.311111111111111, 0.1285140562249, 0.214132762312634, 0.413461538461538, 0.183333333333333, 0.4, 0.4375, 0.167778836987607, 0.25, 0.5, 0.166666666666667, 0.181818181818182, 0.21580547112462, 0.0792452830188679, 0.424657534246575, 0, 0 ), CA11 = c(0.00600600600600601, 0, 0, 0, 0, 0.00401606425702811, 0.012847965738758, 0, 0.05, 0, 0, 0, 0, 0, 0, 0, 0.00911854103343465, 0.0113207547169811, 0.0410958904109589, 0, 0), CA111 = c(0, 0, 0, 0, 0, 0, 0.00499643112062812, 0, 0.0333333333333333, 0, 0, 0, 0, 0, 0, 0, 0.0060790273556231, 0.00754716981132075, 0.0273972602739726, 0, 0), CA1111 = c(0, 0, 0, 0, 0, 0, 0.000713775874375446, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), CA1113 = c(0, 0, 0, 0, 0, 0, 0.000713775874375446, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), CA1115 = c(0, 0, 0, 0, 0, 0, 0.000713775874375446, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), CA1116 = c(0, 0, 0, 0, 0, 0, 0, 0, 0.0166666666666667, 0, 0, 0, 0, 0, 0, 0, 0.00303951367781155, 0.00377358490566038, 0, 0, 0), CA1117 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.0136986301369863, 0, 0), CA112 = c(0, 0, 0, 0, 0, 0, 0.00285510349750178, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), CA1122 = c(0, 0, 0, 0, 0, 0, 0.00142755174875089, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)), class = "data.frame", row.names = c("ND5", "ND6", "ND8/ND10", "ND3", "ND7", "ND2", "ND1", "ND4", "KB3/KB4/KB5", "KB1", "KB2", "IS1", "KB9", "KB7/KB8", "KB6", "IS4", "IS3", "IS2", "KB12/KB14", "KB13", "IS5"))

The function clique_function is supposed to loop around object_list and select the variable type (column) such as CA1 of the three nodes from clique_list.

 clique_function <- function(clique_list, type, object_list) { for (i in 1:ncol(clique_list)) { clique_object <- subset(object_list, row.names(object_list) %in% clique_list[, i], colnames(object_list) == type) } return(clique_object) }

Expected output clique_object is a subset of object_list showing the occurrence of a chosen object type type for all the cliques in clique_list.

For exemple:

clique_object <- structure(list(cliques = c("ND1", "IS1", "IS3", "ND2", "IS1", "IS3", "ND1", "IS4", "IS3", "ND1", "IS1", "IS3", "ND1", "IS1", "IS8", "ND3", "IS1", "IS3", "ND1", "IS1", "IS3"), CA1 = c(0.0007137759, 0.0047664442, 0.009118541, 0.0007137759, 0.0047664442, 0.009118541, 0.0007137759, 0.0047664442, 0.009118541, 0.0007137759, 0.0047664442, 0.009118541, 0.0007137759, 0.0047664442, 0.009118541, 0.0007137759, 0.0047664442, 0.009118541, 0.0007137759, 0.0047664442, 0.009118541 )), class = "data.frame", row.names = c(NA, -21L))

The function works properly if instead of return(clique_object) I put print(clique_object). In the first case I get the full list from the function looping around the data frames. But with return(clique_object) I only get the result for the first clique in clique_list.

I would like the function to output the full result as a data frame.

Thank you.

langtang · Accepted Answer · 2022-02-18 15:03:55Z

If you change you function like this:

clique_function <- function(clique_list, type, object_list) { lapply(seq(1,ncol(clique_list)), function(i) { subset(object_list, row.names(object_list) %in% clique_list[, i],colnames(object_list) == type) }) }

then it will return a list of dataframes like this:

[[1]] CA1 ND1 0.2141328 IS1 0.1677788 IS3 0.2158055 [[2]] CA1 IS1 0.16777884 IS3 0.21580547 IS2 0.07924528 [[3]] CA1 ND2 0.1285141 ND1 0.2141328 IS1 0.1677788

You can then choose how you want to combine these frames. For example, you could combine them like this:

bind_rows(lapply(seq_along(res), function(x) tibble("clique"=x, "nodes"=rownames(res[[x]]), res[[x]]))) # A tibble: 9 x 3 clique nodes CA1 <int> <chr> <dbl> 1 1 ND1 0.214 2 1 IS1 0.168 3 1 IS3 0.216 4 2 IS1 0.168 5 2 IS3 0.216 6 2 IS2 0.0792 7 3 ND2 0.129 8 3 ND1 0.214 9 3 IS1 0.168

but I don't know what your desired output structure is. In actual practice, I would further adjust the clique_function to return the desired final structure in one call.

Waldi · Accepted Answer · 2022-02-18 15:01:30Z

You could fill a clique_object list and use rbind to put the results together in a data.frame:

clique_function <- function(clique_list, type, object_list) { clique_object <- list() for (i in 1:ncol(clique_list)) { clique_object[[i]] <- subset(object_list, row.names(object_list) %in% clique_list[, i], colnames(object_list) == type) } return(do.call(rbind,clique_object)) } clique_function(clique_list,"CA1",object_list) CA1 ND1 0.21413276 IS1 0.16777884 IS3 0.21580547 IS11 0.16777884 IS31 0.21580547 IS2 0.07924528 ND2 0.12851406 ND11 0.21413276 IS12 0.16777884

Collectives™ on Stack Overflow

How to make a loop function output its result as a data frame in R

2 Answers 2

Comments

Comments

Hot Network Questions

Collectives™ on Stack Overflow

2 Answers 2

Comments

Comments

Related