From 5d25b3c3efefb15a87237291c39fba0d2ef929ee Mon Sep 17 00:00:00 2001 From: Bryan Roessler Date: Sun, 29 Sep 2024 18:36:55 -0400 Subject: [PATCH] Add jittering to interaction plots --- .../apps/r/calculate_interaction_zscores.R | 21 ++++++++++--------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/qhtcp-workflow/apps/r/calculate_interaction_zscores.R b/qhtcp-workflow/apps/r/calculate_interaction_zscores.R index 6962a832..2cde11cf 100644 --- a/qhtcp-workflow/apps/r/calculate_interaction_zscores.R +++ b/qhtcp-workflow/apps/r/calculate_interaction_zscores.R @@ -151,12 +151,12 @@ load_and_filter_data <- function(easy_results_file, sd = 3) { OrfRep = if_else(ORF == "YDL227C", "YDL227C", OrfRep), # should these be hardcoded? conc_num = as.numeric(gsub("[^0-9\\.]", "", Conc)), conc_num_factor_new = factor(conc_num), - conc_num_factor_zeroed = factor(as.numeric(conc_num_factor2) - 1), - conc_num_factor = as.numeric(conc_num_factor_zeroed) # for legacy purposes, neither conc_num nor a factor + conc_num_factor_zeroed = factor(as.numeric(conc_num_factor_new) - 1), + conc_num_factor = as.numeric(conc_num_factor_zeroed) # for legacy purposes ) - - return(df) - } + + return(df) +} # Update Gene names using the SGD gene list update_gene_names <- function(df, sgd_gene_list) { @@ -251,10 +251,10 @@ calculate_interaction_scores <- function(df, max_conc, bg_stats, Zscore_AUC = Delta_AUC / WT_sd_AUC, # Fit linear models and store in list-columns - gene_lm_L = list(lm(Delta_L ~ conc_num_factor_zeroed_num, data = pick(everything()))), - gene_lm_K = list(lm(Delta_K ~ conc_num_factor_zeroed_num, data = pick(everything()))), - gene_lm_r = list(lm(Delta_r ~ conc_num_factor_zeroed_num, data = pick(everything()))), - gene_lm_AUC = list(lm(Delta_AUC ~ conc_num_factor_zeroed_num, data = pick(everything()))), + gene_lm_L = list(lm(Delta_L ~ conc_num_factor, data = pick(everything()))), + gene_lm_K = list(lm(Delta_K ~ conc_num_factor, data = pick(everything()))), + gene_lm_r = list(lm(Delta_r ~ conc_num_factor, data = pick(everything()))), + gene_lm_AUC = list(lm(Delta_AUC ~ conc_num_factor, data = pick(everything()))), # Extract coefficients using purrr::map_dbl lm_intercept_L = map_dbl(gene_lm_L, ~ coef(.x)[1]), @@ -763,7 +763,8 @@ generate_interaction_plot_configs <- function(df, limits_map = NULL, plot_type = error_bar = TRUE, x_breaks = unique(df_filtered$conc_num_factor_new), x_labels = as.character(unique(df_filtered$conc_num)), - grid_layout = list(ncol = 2, nrow = 2) + grid_layout = list(ncol = 2, nrow = 2), + position = "jitter" ) configs <- append(configs, list(config)) }