diff --git a/qhtcp-workflow/apps/r/calculate_interaction_zscores.R b/qhtcp-workflow/apps/r/calculate_interaction_zscores.R index f6db17f7..2d1877e5 100644 --- a/qhtcp-workflow/apps/r/calculate_interaction_zscores.R +++ b/qhtcp-workflow/apps/r/calculate_interaction_zscores.R @@ -552,6 +552,7 @@ generate_scatter_plot <- function(plot, config) { return(plot) } + generate_box_plot <- function(plot, config) { plot <- plot + geom_boxplot() @@ -684,18 +685,18 @@ generate_rank_plot_configs <- function(df_filtered, is_lm = FALSE, adjust = FALS configs <- list() # SD-based plots for L and K - for (var in c("L", "K")) { + for (variable in c("L", "K")) { for (sd_band in sd_bands) { # Determine columns based on whether it's lm or not if (is_lm) { - rank_var <- paste0(var, "_Rank_lm") - zscore_var <- paste0("Z_lm_", var) - y_label <- paste("Int Z score", var) + rank_var <- paste0(variable, "_Rank_lm") + zscore_var <- paste0("Z_lm_", variable) + y_label <- paste("Int Z score", variable) } else { - rank_var <- paste0(var, "_Rank") - zscore_var <- paste0("Avg_Zscore_", var) - y_label <- paste("Avg Z score", var) + rank_var <- paste0(variable, "_Rank") + zscore_var <- paste0("Avg_Zscore_", variable) + y_label <- paste("Avg Z score", variable) } # Annotated Plot Configuration @@ -704,7 +705,7 @@ generate_rank_plot_configs <- function(df_filtered, is_lm = FALSE, adjust = FALS x_var = rank_var, y_var = zscore_var, plot_type = "scatter", - title = paste(y_label, "vs. Rank for", var, "above", sd_band, "SD"), + title = paste(y_label, "vs. Rank for", variable, "above", sd_band, "SD"), sd_band = sd_band, annotations = list( list( @@ -729,7 +730,7 @@ generate_rank_plot_configs <- function(df_filtered, is_lm = FALSE, adjust = FALS x_var = rank_var, y_var = zscore_var, plot_type = "scatter", - title = paste(y_label, "vs. Rank for", var, "above", sd_band, "SD No Annotations"), + title = paste(y_label, "vs. Rank for", variable, "above", sd_band, "SD No Annotations"), sd_band = sd_band, annotations = NULL, sd_band_values = sd_band, @@ -739,26 +740,26 @@ generate_rank_plot_configs <- function(df_filtered, is_lm = FALSE, adjust = FALS } } - # Average ZScore and Rank Avg ZScore Plots for r, L, K, and AUC - for (var in variables) { + # Avg ZScore and Rank Avg ZScore Plots for r, L, K, and AUC + for (variable in variables) { for (plot_type in c("Avg_Zscore_vs_lm", "Rank_Avg_Zscore_vs_lm")) { # Define x and y variables based on plot type if (plot_type == "Avg_Zscore_vs_lm") { - x_var <- paste0("Avg_Zscore_", var) - y_var <- paste0("Z_lm_", var) - title_suffix <- paste("Avg Zscore vs lm", var) + x_var <- paste0("Avg_Zscore_", variable) + y_var <- paste0("Z_lm_", variable) + title_suffix <- paste("Avg Zscore vs lm", variable) } else if (plot_type == "Rank_Avg_Zscore_vs_lm") { - x_var <- paste0(var, "_Rank") - y_var <- paste0(var, "_Rank_lm") - title_suffix <- paste("Rank Avg Zscore vs lm", var) + x_var <- paste0(variable, "_Rank") + y_var <- paste0(variable, "_Rank_lm") + title_suffix <- paste("Rank Avg Zscore vs lm", variable) } # Determine y-axis label if (plot_type == "Avg_Zscore_vs_lm") { - y_label <- paste("Z lm", var) + y_label <- paste("Z lm", variable) } else { - y_label <- paste("Rank lm", var) + y_label <- paste("Rank lm", variable) } # Determine correlation text (R-squared)