Use cartesian limits for plots
Tento commit je obsažen v:
@@ -281,9 +281,12 @@ calculate_interaction_scores <- function(df, max_conc, variables, group_vars = c
|
||||
lm_AUC <- lm(Delta_AUC ~ conc_num_factor, data = stats)
|
||||
|
||||
interactions <- stats %>%
|
||||
transmute(
|
||||
summarise(
|
||||
OrfRep = first(OrfRep),
|
||||
Gene = first(Gene),
|
||||
num = first(num),
|
||||
conc_num = first(conc_num),
|
||||
conc_num_factor = first(conc_num_factor),
|
||||
Raw_Shift_L = first(Raw_Shift_L),
|
||||
Raw_Shift_K = first(Raw_Shift_K),
|
||||
Raw_Shift_r = first(Raw_Shift_r),
|
||||
@@ -352,9 +355,26 @@ calculate_interaction_scores <- function(df, max_conc, variables, group_vars = c
|
||||
|
||||
calculations_joined <- df %>% select(-any_of(setdiff(names(calculations), c("OrfRep", "Gene", "num", "conc_num", "conc_num_factor"))))
|
||||
calculations_joined <- left_join(calculations_joined, calculations, by = c("OrfRep", "Gene", "num", "conc_num", "conc_num_factor"))
|
||||
|
||||
|
||||
|
||||
# # TODO for debug
|
||||
# df_duplicates <- df %>%
|
||||
# group_by(OrfRep, Gene, num) %>%
|
||||
# filter(n() > 1)
|
||||
|
||||
# interactions_duplicates <- interactions %>%
|
||||
# group_by(OrfRep, Gene, num) %>%
|
||||
# filter(n() > 1)
|
||||
|
||||
# print(df_duplicates)
|
||||
# print(interactions_duplicates)
|
||||
|
||||
|
||||
interactions_joined <- df %>% select(-any_of(setdiff(names(interactions), c("OrfRep", "Gene", "num"))))
|
||||
interactions_joined <- left_join(interactions_joined, interactions, by = c("OrfRep", "Gene", "num"))
|
||||
|
||||
|
||||
interactions_joined <- df %>% select(-any_of(setdiff(names(interactions), c("OrfRep", "Gene", "num", "conc_num", "conc_num_factor"))))
|
||||
interactions_joined <- left_join(interactions_joined, interactions, by = c("OrfRep", "Gene", "num", "conc_num", "conc_num_factor"))
|
||||
|
||||
return(list(calculations = calculations, interactions = interactions, interactions_joined = interactions_joined,
|
||||
calculations_joined = calculations_joined))
|
||||
@@ -420,7 +440,20 @@ generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_la
|
||||
}
|
||||
|
||||
generate_scatter_plot <- function(plot, config, interactive = FALSE) {
|
||||
|
||||
# Check for missing or out-of-range data
|
||||
missing_data <- config$df %>%
|
||||
filter(
|
||||
is.na(!!sym(config$x_var)) | is.na(!!sym(config$y_var)) |
|
||||
!!sym(config$y_var) < min(config$ylim_vals, na.rm = TRUE) |
|
||||
!!sym(config$y_var) > max(config$ylim_vals, na.rm = TRUE)
|
||||
)
|
||||
|
||||
# Print the rows with missing or out-of-range data if any
|
||||
if (nrow(missing_data) > 0) {
|
||||
message("Missing or out-of-range data for ", config$title, ":")
|
||||
print(missing_data %>% select(any_of(c("OrfRep", "Gene", "num", "conc_num", "conc_num_factor", config$x_var, config$y_var))), n = 100)
|
||||
}
|
||||
|
||||
# Add the interactive `text` aesthetic if `interactive` is TRUE
|
||||
if (interactive) {
|
||||
plot <- if (!is.null(config$delta_bg_point) && config$delta_bg_point) {
|
||||
@@ -475,34 +508,16 @@ generate_scatter_plot <- function(plot, config, interactive = FALSE) {
|
||||
labels = config$x_labels)
|
||||
}
|
||||
|
||||
# Add y-axis limits if specified
|
||||
# Use coord_cartesian for zooming in without removing data outside the range
|
||||
if (!is.null(config$coord_cartesian)) {
|
||||
plot <- plot + coord_cartesian(ylim = config$coord_cartesian)
|
||||
}
|
||||
|
||||
# Use scale_y_continuous for setting the y-axis limits
|
||||
if (!is.null(config$ylim_vals)) {
|
||||
plot <- plot + scale_y_continuous(limits = config$ylim_vals)
|
||||
}
|
||||
|
||||
# Add Cartesian coordinates customization if specified
|
||||
if (!is.null(config$coord_cartesian)) {
|
||||
plot <- plot + coord_cartesian(ylim = config$coord_cartesian)
|
||||
}
|
||||
|
||||
return(plot)
|
||||
}
|
||||
|
||||
generate_box_plot <- function(plot, config) {
|
||||
plot <- plot + geom_boxplot()
|
||||
|
||||
if (!is.null(config$x_breaks) && !is.null(config$x_labels) && !is.null(config$x_label)) {
|
||||
plot <- plot + scale_x_discrete(
|
||||
name = config$x_label,
|
||||
breaks = config$x_breaks,
|
||||
labels = config$x_labels
|
||||
)
|
||||
}
|
||||
|
||||
if (!is.null(config$coord_cartesian)) {
|
||||
plot <- plot + coord_cartesian(ylim = config$coord_cartesian)
|
||||
}
|
||||
|
||||
return(plot)
|
||||
}
|
||||
|
||||
@@ -562,14 +577,13 @@ generate_interaction_plot_configs <- function(df, variables) {
|
||||
# Dynamically generate the names of the columns
|
||||
var_info <- list(
|
||||
ylim = limits_map[[variable]],
|
||||
lm_model = df[[paste0("lm_", variable)]][[1]],
|
||||
sd_col = paste0("WT_sd_", variable),
|
||||
sd_col = paste0("WT_sd_", variable)
|
||||
)
|
||||
|
||||
# Extract the precomputed linear model coefficients
|
||||
lm_line <- list(
|
||||
intercept = coef(var_info$lm_model)[1],
|
||||
slope = coef(var_info$lm_model)[2]
|
||||
intercept = df[[paste0("lm_intercept_", variable)]],
|
||||
slope = df[[paste0("lm_slope_", variable)]]
|
||||
)
|
||||
|
||||
annotations <- lapply(names(annotation_positions[[variable]]), function(annotation_name) {
|
||||
@@ -669,7 +683,6 @@ generate_rank_plot_configs <- function(df, rank_var, zscore_var, var, is_lm = FA
|
||||
return(configs)
|
||||
}
|
||||
|
||||
|
||||
generate_correlation_plot_configs <- function(df, variables) {
|
||||
configs <- list()
|
||||
|
||||
@@ -960,16 +973,16 @@ main <- function() {
|
||||
)
|
||||
)
|
||||
|
||||
message("Generating quality control plots")
|
||||
generate_and_save_plots(out_dir_qc, "L_vs_K_before_quality_control", l_vs_k_plots)
|
||||
generate_and_save_plots(out_dir_qc, "frequency_delta_background", frequency_delta_bg_plots)
|
||||
generate_and_save_plots(out_dir_qc, "L_vs_K_above_threshold", above_threshold_plots)
|
||||
generate_and_save_plots(out_dir_qc, "plate_analysis", plate_analysis_plots)
|
||||
generate_and_save_plots(out_dir_qc, "plate_analysis_boxplots", plate_analysis_boxplots)
|
||||
generate_and_save_plots(out_dir_qc, "plate_analysis_no_zeros", plate_analysis_no_zeros_plots)
|
||||
generate_and_save_plots(out_dir_qc, "plate_analysis_no_zeros_boxplots", plate_analysis_no_zeros_boxplots)
|
||||
generate_and_save_plots(out_dir_qc, "L_vs_K_for_strains_2SD_outside_mean_K", l_outside_2sd_k_plots)
|
||||
generate_and_save_plots(out_dir_qc, "delta_background_vs_K_for_strains_2sd_outside_mean_K", delta_bg_outside_2sd_k_plots)
|
||||
# message("Generating quality control plots")
|
||||
# generate_and_save_plots(out_dir_qc, "L_vs_K_before_quality_control", l_vs_k_plots)
|
||||
# generate_and_save_plots(out_dir_qc, "frequency_delta_background", frequency_delta_bg_plots)
|
||||
# generate_and_save_plots(out_dir_qc, "L_vs_K_above_threshold", above_threshold_plots)
|
||||
# generate_and_save_plots(out_dir_qc, "plate_analysis", plate_analysis_plots)
|
||||
# generate_and_save_plots(out_dir_qc, "plate_analysis_boxplots", plate_analysis_boxplots)
|
||||
# generate_and_save_plots(out_dir_qc, "plate_analysis_no_zeros", plate_analysis_no_zeros_plots)
|
||||
# generate_and_save_plots(out_dir_qc, "plate_analysis_no_zeros_boxplots", plate_analysis_no_zeros_boxplots)
|
||||
# generate_and_save_plots(out_dir_qc, "L_vs_K_for_strains_2SD_outside_mean_K", l_outside_2sd_k_plots)
|
||||
# generate_and_save_plots(out_dir_qc, "delta_background_vs_K_for_strains_2sd_outside_mean_K", delta_bg_outside_2sd_k_plots)
|
||||
|
||||
# Clean up
|
||||
rm(df, df_above_tolerance, df_no_zeros, df_no_zeros_stats, df_no_zeros_filtered_stats, ss)
|
||||
|
||||
Odkázat v novém úkolu
Zablokovat Uživatele