From 4f90330500b3da4ef015cd10b17dd4de3c93a81e Mon Sep 17 00:00:00 2001 From: Bryan Roessler Date: Mon, 16 Sep 2024 12:27:24 -0400 Subject: [PATCH] Simplify R Squared calculations --- .../apps/r/calculate_interaction_zscores.R | 20 ++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/qhtcp-workflow/apps/r/calculate_interaction_zscores.R b/qhtcp-workflow/apps/r/calculate_interaction_zscores.R index aa93e1e0..6f8de734 100644 --- a/qhtcp-workflow/apps/r/calculate_interaction_zscores.R +++ b/qhtcp-workflow/apps/r/calculate_interaction_zscores.R @@ -1231,6 +1231,7 @@ main <- function() { generate_and_save_plots(output_dir = out_dir, file_name = "RankPlots", plot_configs = rank_plot_configs, grid_layout = list(ncol = 3, nrow = 2)) + message("Generating ranked linear model plots") # Generate rank plots for L and K using linear model (`lm`) ranks rank_lm_plot_configs <- generate_rank_plot_configs( df = zscores_interactions, @@ -1243,7 +1244,7 @@ main <- function() { generate_and_save_plots(output_dir = out_dir, file_name = "RankPlots_lm", plot_configs = rank_lm_plot_configs, grid_layout = list(ncol = 3, nrow = 2)) - message("Filtering and regenerating rank plots") + message("Filtering and reranking plots") # Filter rows where either Z_lm_L or Avg_Zscore_L is not NA # Formerly X_NArm zscores_interactions_filtered <- zscores_interactions %>% @@ -1252,10 +1253,10 @@ main <- function() { ungroup() %>% rowwise() %>% mutate( - lm_R_squared_L = if (n() > 1) summary(lm(Z_lm_L ~ Avg_Zscore_L))$r.squared else NA, - lm_R_squared_K = if (n() > 1) summary(lm(Z_lm_K ~ Avg_Zscore_K))$r.squared else NA, - lm_R_squared_r = if (n() > 1) summary(lm(Z_lm_r ~ Avg_Zscore_r))$r.squared else NA, - lm_R_squared_AUC = if (n() > 1) summary(lm(Z_lm_AUC ~ Avg_Zscore_AUC))$r.squared else NA, + lm_R_squared_L = summary(lm(Z_lm_L ~ Avg_Zscore_L))$r.squared, + lm_R_squared_K = summary(lm(Z_lm_K ~ Avg_Zscore_K))$r.squared, + lm_R_squared_r = summary(lm(Z_lm_r ~ Avg_Zscore_r))$r.squared, + lm_R_squared_AUC = summary(lm(Z_lm_AUC ~ Avg_Zscore_AUC))$r.squared, Overlap = case_when( Z_lm_L >= 2 & Avg_Zscore_L >= 2 ~ "Deletion Enhancer Both", @@ -1269,23 +1270,24 @@ main <- function() { ) %>% ungroup() - message("Generating filtered rank plots") + message("Generating filtered ranked plots") rank_plot_filtered_configs <- generate_rank_plot_configs( df = zscores_interactions_filtered, interaction_vars = interaction_vars, is_lm = FALSE, adjust = FALSE - )$plot_configs + ) generate_and_save_plots(output_dir = out_dir, file_name = "RankPlots_na_rm", plot_configs = rank_plot_filtered_configs, grid_layout = list(ncol = 3, nrow = 2)) - + + message("Generating filtered ranked linear model plots") rank_plot_lm_filtered_configs <- generate_rank_plot_configs( df = zscores_interactions_filtered, interaction_vars = interaction_vars, is_lm = TRUE, adjust = FALSE - )$plot_configs + ) generate_and_save_plots(output_dir = out_dir, file_name = "RankPlots_lm_na_rm", plot_configs = rank_plot_lm_filtered_configs, grid_layout = list(ncol = 3, nrow = 2))