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Avoid get() in across_all

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Bryan Roessler
2024-09-15 11:05:55 -04:00
parent 2531a739dd
commit 4877c1413e
1 changed files with 23 additions and 10 deletions
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33
qhtcp-workflow/apps/r/calculate_interaction_zscores.R
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@@ -602,16 +602,29 @@ generate_box_plot <- function(plot, config) {
# Adjust missing values and calculate ranks # Adjust missing values and calculate ranks
adjust_missing_and_rank <- function(df, variables) { adjust_missing_and_rank <- function(df, variables) {
# Adjust missing values in Avg_Zscore and Z_lm columns, and apply rank to the specified variables # Loop over each variable
df <- df %>% for (var in variables) {
mutate(across(all_of(variables), list( # Construct column names
Avg_Zscore = ~ if_else(is.na(get(paste0("Avg_Zscore_", cur_column()))), 0.001, get(paste0("Avg_Zscore_", cur_column()))), avg_zscore_col <- paste0("Avg_Zscore_", var)
Z_lm = ~ if_else(is.na(get(paste0("Z_lm_", cur_column()))), 0.001, get(paste0("Z_lm_", cur_column()))), z_lm_col <- paste0("Z_lm_", var)
Rank = ~ rank(get(paste0("Avg_Zscore_", cur_column()))), rank_col <- paste0("Rank_", var)
Rank_lm = ~ rank(get(paste0("Z_lm_", cur_column()))) rank_lm_col <- paste0("Rank_lm_", var)
), .names = "{fn}_{col}"))
# Check if the columns exist in the data frame
if (all(c(avg_zscore_col, z_lm_col) %in% names(df))) {
# Adjust missing values by replacing NA with 0.001
df[[avg_zscore_col]] <- if_else(is.na(df[[avg_zscore_col]]), 0.001, df[[avg_zscore_col]])
df[[z_lm_col]] <- if_else(is.na(df[[z_lm_col]]), 0.001, df[[z_lm_col]])
# Compute ranks and create new columns
df[[rank_col]] <- rank(df[[avg_zscore_col]], na.last = "keep")
df[[rank_lm_col]] <- rank(df[[z_lm_col]], na.last = "keep")
} else {
warning(paste("Columns", avg_zscore_col, "or", z_lm_col, "not found in data frame"))
}
}
return(df) return(df)
} }