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@@ -151,12 +151,12 @@ load_and_filter_data <- function(easy_results_file, sd = 3) {
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OrfRep = if_else(ORF == "YDL227C", "YDL227C", OrfRep), # should these be hardcoded?
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conc_num = as.numeric(gsub("[^0-9\\.]", "", Conc)),
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conc_num_factor_new = factor(conc_num),
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- conc_num_factor_zeroed = factor(as.numeric(conc_num_factor2) - 1),
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- conc_num_factor = as.numeric(conc_num_factor_zeroed) # for legacy purposes, neither conc_num nor a factor
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+ conc_num_factor_zeroed = factor(as.numeric(conc_num_factor_new) - 1),
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+ conc_num_factor = as.numeric(conc_num_factor_zeroed) # for legacy purposes
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)
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-
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- return(df)
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- }
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+
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+ return(df)
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+}
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# Update Gene names using the SGD gene list
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update_gene_names <- function(df, sgd_gene_list) {
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@@ -251,10 +251,10 @@ calculate_interaction_scores <- function(df, max_conc, bg_stats,
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Zscore_AUC = Delta_AUC / WT_sd_AUC,
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# Fit linear models and store in list-columns
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- gene_lm_L = list(lm(Delta_L ~ conc_num_factor_zeroed_num, data = pick(everything()))),
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- gene_lm_K = list(lm(Delta_K ~ conc_num_factor_zeroed_num, data = pick(everything()))),
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- gene_lm_r = list(lm(Delta_r ~ conc_num_factor_zeroed_num, data = pick(everything()))),
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- gene_lm_AUC = list(lm(Delta_AUC ~ conc_num_factor_zeroed_num, data = pick(everything()))),
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+ gene_lm_L = list(lm(Delta_L ~ conc_num_factor, data = pick(everything()))),
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+ gene_lm_K = list(lm(Delta_K ~ conc_num_factor, data = pick(everything()))),
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+ gene_lm_r = list(lm(Delta_r ~ conc_num_factor, data = pick(everything()))),
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+ gene_lm_AUC = list(lm(Delta_AUC ~ conc_num_factor, data = pick(everything()))),
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# Extract coefficients using purrr::map_dbl
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lm_intercept_L = map_dbl(gene_lm_L, ~ coef(.x)[1]),
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@@ -763,7 +763,8 @@ generate_interaction_plot_configs <- function(df, limits_map = NULL, plot_type =
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error_bar = TRUE,
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x_breaks = unique(df_filtered$conc_num_factor_new),
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x_labels = as.character(unique(df_filtered$conc_num)),
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- grid_layout = list(ncol = 2, nrow = 2)
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+ grid_layout = list(ncol = 2, nrow = 2),
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+ position = "jitter"
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)
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configs <- append(configs, list(config))
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}
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