Skip to content

Fix compound duplication #39

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
GregJohnsonJr merged 4 commits into from
Mar 11, 2025
Merged

Fix compound duplication #39

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
b74129e
Fix for #35
GregJohnsonJr Mar 10, 2025
54c2d74
Added Test data, and new test for the new unique_compounds function.
GregJohnsonJr Mar 10, 2025
08af3b1
Making unique duplicates a recursive function. It is possible that ad…
GregJohnsonJr Mar 11, 2025
6a619a0
Squashed commit of the following:
GregJohnsonJr Mar 11, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
16 changes: 13 additions & 3 deletions R/import_data.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -97,19 +97,29 @@ import_data <- function(peak_table, meta_data, format = "none") {
}


unique_compounds <- function(peak_table_list) {
unique_compounds <- function(peak_table_list, show_message = TRUE) {
peak_table <- peak_table_list$peak_table
duplicates <- names(which(table(peak_table$Compound) > 1))
if(length(duplicates) > 0){
if(length(duplicates) > 0 && show_message){
cli::cli_inform("Found duplicate compound values, will add a suffix to unique
the value.")
the value.")
}
for(name in duplicates) {
idx <- which(peak_table$Compound == name)
for(i in seq(length(idx))){
peak_table$Compound[[idx[[i]]]] <- paste0(peak_table$Compound[[idx[[i]]]], "_", i)
}
}

# Recursive call to ensure there are no duplicates after fix
duplicates <- names(which(table(peak_table$Compound) > 1))

if(length(duplicates) > 0){
peak_table <- unique_compounds(list(
"peak_table" = peak_table,
"raw_table" = peak_table
), FALSE)$peak_table
}
return(list(
"peak_table" = peak_table,
"raw_table" = peak_table
Expand Down
8 changes: 8 additions & 0 deletions tests/testthat/test-import_data.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,14 @@ test_that("unique_compounds annotate duplicates properly", {
length(uniqued_list$raw_table$Compound))

expect_false(length(unique(df$Compound)) == length(df$Compound))

df <- data.frame(Compound = c("1", "1", "1_1", "1_1_1"))
ls <- list(peak_table = df, raw_table = df)
uniqued_list <- unique_compounds(ls)

expect_true(uniqued_list$peak_table$Compound[[4]] == "1_1_1_2")
expect_true(uniqued_list$peak_table$Compound[[1]] == "1_1_1_1")

})