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Loosen R linter

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Bryan Roessler
2024-09-10 14:19:44 -04:00
parent 9986d138b3
commit 324a4a15d5
2 changed files with 20 additions and 8 deletions
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1
qhtcp-workflow/.lintr
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@@ -1,4 +1,5 @@
linters: linters_with_defaults( linters: linters_with_defaults(
object_length_linter = object_length_linter(40),
object_name_linter = NULL, object_name_linter = NULL,
object_usage_linter = NULL, object_usage_linter = NULL,
commented_code_linter = NULL, commented_code_linter = NULL,

27
qhtcp-workflow/apps/r/calculate_interaction_zscores.R
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@@ -514,9 +514,12 @@ generate_interaction_plot_configs <- function(df, variables) {
return(plot_configs) return(plot_configs)
} }
generate_rank_plot_config <- function(df, rank_var, zscore_var, label_prefix) { generate_rank_plot_configs <- function(df, rank_var, zscore_var, label_prefix, is_lm = FALSE) {
configs <- list() configs <- list()
# Adjust titles for _lm plots if is_lm is TRUE
plot_title_prefix <- if (is_lm) "Interaction Z score vs. Rank for" else "Average Z score vs. Rank for"
for (sd_band in c(1, 2, 3)) { for (sd_band in c(1, 2, 3)) {
# Annotated version (with text) # Annotated version (with text)
configs[[length(configs) + 1]] <- list( configs[[length(configs) + 1]] <- list(
@@ -524,7 +527,7 @@ generate_rank_plot_config <- function(df, rank_var, zscore_var, label_prefix) {
x_var = rank_var, x_var = rank_var,
y_var = zscore_var, y_var = zscore_var,
plot_type = "rank", plot_type = "rank",
title = paste("Average Z score vs. Rank for", label_prefix, "above", sd_band, "SD"), title = paste(plot_title_prefix, label_prefix, "above", sd_band, "SD"),
sd_band = sd_band, sd_band = sd_band,
enhancer_label = list( enhancer_label = list(
x = nrow(df) / 2, y = 10, x = nrow(df) / 2, y = 10,
@@ -542,16 +545,17 @@ generate_rank_plot_config <- function(df, rank_var, zscore_var, label_prefix) {
x_var = rank_var, x_var = rank_var,
y_var = zscore_var, y_var = zscore_var,
plot_type = "rank", plot_type = "rank",
title = paste("Average Z score vs. Rank for", label_prefix, "above", sd_band, "SD"), title = paste(plot_title_prefix, label_prefix, "above", sd_band, "SD"),
sd_band = sd_band, sd_band = sd_band,
enhancer_label = NULL, # Remove annotations for _notext enhancer_label = NULL, # No annotations for _notext
suppressor_label = NULL # Remove annotations for _notext suppressor_label = NULL # No annotations for _notext
) )
} }
return(configs) return(configs)
} }
# Generate all rank plot configurations for L and K (annotated and _notext) # Generate all rank plot configurations for L and K (annotated and _notext)
rank_plot_config <- c( rank_plot_config <- c(
create_rank_plot_config(zscores_interactions_adjusted, "L_Rank", "Avg_Zscore_L", "L"), create_rank_plot_config(zscores_interactions_adjusted, "L_Rank", "Avg_Zscore_L", "L"),
@@ -928,16 +932,23 @@ main <- function() {
zscores_interactions_adjusted <- adjust_missing_and_rank(zscores_interactions) zscores_interactions_adjusted <- adjust_missing_and_rank(zscores_interactions)
# Generate all rank plot configurations for L and K
rank_plot_configs <- c( rank_plot_configs <- c(
generate_rank_plot_configs(zscores_interactions_adjusted, "Rank_L", "Avg_Zscore_L", "L"), generate_rank_plot_configs(zscores_interactions_adjusted, "Rank_L", "Avg_Zscore_L", "L"),
generate_rank_plot_configs(zscores_interactions_adjusted, "Rank_K", "Avg_Zscore_K", "K") generate_rank_plot_configs(zscores_interactions_adjusted, "Rank_K", "Avg_Zscore_K", "K")
) )
# Generate and save rank plots
generate_and_save_plots(output_dir = out_dir, file_name = "RankPlots", generate_and_save_plots(output_dir = out_dir, file_name = "RankPlots",
plot_configs = rank_plot_config, grid_layout = list(ncol = 3, nrow = 2)) plot_configs = rank_plot_config, grid_layout = list(ncol = 3, nrow = 2))
rank_lm_plot_config <- c(
generate_rank_lm_plot_configs(zscores_interactions_adjusted, "Rank_lm_L", "Z_lm_L", "L"),
generate_rank_lm_plot_configs(zscores_interactions_adjusted, "Rank_lm_K", "Z_lm_K", "K")
)
generate_and_save_plots(output_dir = out_dir, file_name = "RankPlots_lm",
plot_configs = rank_lm_plot_config, grid_layout = list(ncol = 3, nrow = 2))
# # Correlation plots # # Correlation plots
# lm_list <- list( # lm_list <- list(
# lm(Z_lm_K ~ Z_lm_L, data = zscores_interactions_filtered), # lm(Z_lm_K ~ Z_lm_L, data = zscores_interactions_filtered),