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Remove superfluous filter function

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This commit is contained in:
Bryan Roessler
2024-09-25 02:12:06 -04:00
parent fbbe351cbb
commit ad6e10e67d
1 changed files with 6 additions and 35 deletions
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41
qhtcp-workflow/apps/r/calculate_interaction_zscores.R
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@@ -656,7 +656,11 @@ generate_interaction_plot_configs <- function(df, variables) {
AUC = c(-6500, 6500) AUC = c(-6500, 6500)
) )
df_filtered <- filter_data(df, variables, filter_na = TRUE, limits_map = limits_map) # Filtering out NAs and outlying values
df_filtered <- df %>%
filter(across(names(limits_map),
~ !is.na(.x) &
between(.x, limits_map[[.names]][1], limits_map[[.names]][2])))
# Define annotation label functions # Define annotation label functions
generate_annotation_labels <- function(df, var, annotation_name) { generate_annotation_labels <- function(df, var, annotation_name) {
@@ -747,7 +751,7 @@ generate_interaction_plot_configs <- function(df, variables) {
return(configs) return(configs)
} }
generate_rank_plot_configs <- function(df, variables, is_lm = FALSE, overlap_color = FALSE) { generate_rank_plot_configs <- function(df, variables, is_lm = FALSE, adjust = FALSE, overlap_color = FALSE) {
sd_bands <- c(1, 2, 3) sd_bands <- c(1, 2, 3)
@@ -977,39 +981,6 @@ generate_correlation_plot_configs <- function(df) {
return(configs) return(configs)
} }
filter_data <- function(df, variables, filter_nf = FALSE, filter_na = FALSE, limits_map = NULL) {
avg_zscore_cols <- paste0("Avg_Zscore_", variables)
z_lm_cols <- paste0("Z_lm_", variables)
rank_avg_zscore_cols <- paste0("Rank_", variables)
rank_z_lm_cols <- paste0("Rank_lm_", variables)
if (filter_nf) {
message("Filtering non-finite values")
df <- df %>%
filter(if_all(all_of(variables), ~ is.finite(.)))
}
if (filter_na) {
message("Filtering NA values")
df <- df %>%
filter(if_all(all_of(variables), ~ !is.na(.)))
}
if (!is.null(limits_map)) {
message("Filtering data outside y-limits (for plotting)")
for (variable in names(limits_map)) {
if (variable %in% variables) {
ylim_vals <- limits_map[[variable]]
df <- df %>%
filter(.data[[variable]] >= ylim_vals[1] & .data[[variable]] <= ylim_vals[2])
}
}
}
return(df)
}
main <- function() { main <- function() {
lapply(names(args$experiments), function(exp_name) { lapply(names(args$experiments), function(exp_name) {
exp <- args$experiments[[exp_name]] exp <- args$experiments[[exp_name]]