From eb2e1ae7d69b25ea7861418b74596b490896181a Mon Sep 17 00:00:00 2001 From: Bryan Roessler Date: Sun, 15 Sep 2024 18:37:42 -0400 Subject: [PATCH] Add some debug for rank plots --- .../apps/r/calculate_interaction_zscores.R | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/qhtcp-workflow/apps/r/calculate_interaction_zscores.R b/qhtcp-workflow/apps/r/calculate_interaction_zscores.R index 16e2d416..67e24870 100644 --- a/qhtcp-workflow/apps/r/calculate_interaction_zscores.R +++ b/qhtcp-workflow/apps/r/calculate_interaction_zscores.R @@ -585,13 +585,16 @@ adjust_missing_and_rank <- function(df, variables) { 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") + df[[rank_col]] <- rank(df[[avg_zscore_col]]) + df[[rank_lm_col]] <- rank(df[[z_lm_col]]) } else { warning(paste("Columns", avg_zscore_col, "or", z_lm_col, "not found in data frame")) } + # Print some debugging output + print(df %>% select("OrfRep", "Gene", "conc_num", "conc_num_factor", + avg_zscore_col, z_lm_col, rank_col, rank_lm_col)) } - + return(df) } @@ -771,8 +774,7 @@ generate_rank_plot_configs <- function(df, rank_var, zscore_var, var, is_lm = FA enhancer_label = NULL, suppressor_label = NULL, shape = 3, - size = 0.1, - position = "jitter" + size = 0.1 ) return(configs) @@ -1213,8 +1215,10 @@ main <- function() { file = file.path(out_dir, "ZScores_Interaction_Deletion_Suppressors_K_lm.csv"), row.names = FALSE) # TODO needs explanation + message("Adjusting and ranking interactions scores") zscores_interactions_adjusted <- adjust_missing_and_rank(zscores_interactions, variables = interaction_vars) + message("Generating rank plots") 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_K", "Avg_Zscore_K", "K")