bryan/hartman-server
1
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity

Fix rank vars names

Browse Source
This commit is contained in:
Bryan Roessler
2024-09-17 16:56:12 -04:00
parent 62cf10860a
commit eb1c04bbab
1 changed files with 28 additions and 20 deletions
Download Patch File Download Diff File Expand all files Collapse all files

48
qhtcp-workflow/apps/r/calculate_interaction_zscores.R
View File

@@ -727,7 +727,7 @@ generate_interaction_plot_configs <- function(df, variables) {
# Box plot config
configs[[length(configs) + 1]] <- modifyList(plot_settings, list(
plot_type = "box",
title = sprintf("%s %s (Boxplot)", df_filtered$OrfRep[1], df_filtered$Gene[1]),
title = sprintf("%s %s (box plot)", df_filtered$OrfRep[1], df_filtered$Gene[1]),
error_bar = FALSE
))
}
@@ -746,11 +746,11 @@ generate_rank_plot_configs <- function(df_filtered, variables, is_lm = FALSE) {
for (sd_band in sd_bands) {
# Determine columns based on whether it's lm or not
if (is_lm) {
rank_var <- paste0(variable, "_Rank_lm")
rank_var <- paste0("Rank_lm_", variable)
zscore_var <- paste0("Z_lm_", variable)
y_label <- paste("Int Z score", variable)
} else {
rank_var <- paste0(variable, "_Rank")
rank_var <- paste0("Rank_", variable)
zscore_var <- paste0("Avg_Zscore_", variable)
y_label <- paste("Avg Z score", variable)
}
@@ -819,19 +819,27 @@ generate_rank_plot_configs <- function(df_filtered, variables, is_lm = FALSE) {
)
)
} else {
x_var <- paste0(variable, "_Rank")
y_var <- paste0(variable, "_Rank_lm")
x_var <- paste0("Rank", variable)
y_var <- paste0("Rank_lm_", variable)
title_suffix <- paste("Rank Avg Zscore vs lm", variable)
rectangles <- NULL
}
print(df_filtered %>% select(all_of(c(x_var, y_var))))
# Check if there is sufficient variation
if (length(unique(df_filtered[[x_var]])) < 2 || length(unique(df_filtered[[y_var]])) < 2) {
message("Not enough variation in ", x_var, " or ", y_var, " to fit linear model. Skipping.")
next
}
# Fit linear model
lm_fit <- lm(df_filtered[[y_var]] ~ df_filtered[[x_var]], data = df_filtered)
# Check for perfect fit
if (summary(lm_fit)$sigma == 0) {
next # Skip this iteration if the fit is perfect
}
# # Check for perfect fit
# if (summary(lm_fit)$sigma == 0) {
# next # Skip this iteration if the fit is perfect
# }
r_squared <- summary(lm_fit)$r.squared
@@ -1158,7 +1166,7 @@ main <- function() {
df_after = df_na_filtered_stats,
)
plate_analysis_box_plot_configs <- generate_plate_analysis_plot_configs(
plate_analysis_boxplot_configs <- generate_plate_analysis_plot_configs(
variables = summary_vars,
df_before = df_filtered_stats,
df_after = df_na_filtered_stats,
@@ -1206,16 +1214,16 @@ 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_plot_configs)
generate_and_save_plots(out_dir_qc, "plate_analysis_boxplots", plate_analysis_boxplot_configs)
generate_and_save_plots(out_dir_qc, "plate_analysis_no_zeros", plate_analysis_no_zeros_plot_configs)
generate_and_save_plots(out_dir_qc, "plate_analysis_no_zeros_boxplots", plate_analysis_no_zeros_boxplot_configs)
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_plot_configs)
# generate_and_save_plots(out_dir_qc, "plate_analysis_boxplots", plate_analysis_boxplot_configs)
# generate_and_save_plots(out_dir_qc, "plate_analysis_no_zeros", plate_analysis_no_zeros_plot_configs)
# generate_and_save_plots(out_dir_qc, "plate_analysis_no_zeros_boxplots", plate_analysis_no_zeros_boxplot_configs)
# 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)
# Process background strains
bg_strains <- c("YDL227C")