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Add configurable page dimensions

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This commit is contained in:
Bryan Roessler
2024-10-04 16:41:33 -04:00
parent 320338316c
commit 20c6e94727
1 changed files with 34 additions and 45 deletions
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79
qhtcp-workflow/apps/r/calculate_interaction_zscores.R
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@@ -20,13 +20,9 @@ suppressPackageStartupMessages({
library("purrr")
})
# Turn all warnings into errors for development
options(warn = 2)
# Constants for configuration
plot_width <- 14
plot_height <- 9
base_size <- 14
parse_arguments <- function() {
args <- if (interactive()) {
c(
@@ -515,7 +511,7 @@ calculate_interaction_scores <- function(df, df_bg, group_vars, overlap_threshol
))
}
generate_and_save_plots <- function(out_dir, filename, plot_configs) {
generate_and_save_plots <- function(out_dir, filename, plot_configs, page_width = 12, page_height = 8) {
message("Generating ", filename, ".pdf and ", filename, ".html")
# Check if we're dealing with multiple plot groups
@@ -526,7 +522,7 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs) {
}
# Open the PDF device once for all plots
pdf(file.path(out_dir, paste0(filename, ".pdf")), width = 16, height = 9)
pdf(file.path(out_dir, paste0(filename, ".pdf")), width = page_width, height = page_height)
# Loop through each plot group
for (group in plot_groups) {
@@ -1043,7 +1039,7 @@ generate_interaction_plot_configs <- function(df, type) {
return(list(
list(grid_layout = list(ncol = 2), plots = stats_plot_configs),
list(grid_layout = list(ncol = 2), plots = stats_boxplot_configs),
list(grid_layout = list(ncol = 4), plots = delta_plot_configs) # nrow calculated dynamically
list(grid_layout = list(ncol = 4), plots = delta_plot_configs[1:12]) # nrow calculated dynamically
))
}
@@ -1123,12 +1119,7 @@ generate_rank_plot_configs <- function(df, is_lm = FALSE, adjust = FALSE, overla
}
}
# Calculate dynamic grid layout based on the number of plots
grid_ncol <- 3
num_plots <- length(plot_configs)
grid_nrow <- ceiling(num_plots / grid_ncol) # Automatically calculate the number of rows
return(list(grid_layout = list(ncol = grid_ncol, nrow = grid_nrow), plots = plot_configs))
return(list(grid_layout = list(ncol = 3), plots = plot_configs))
}
generate_correlation_plot_configs <- function(df, correlation_stats) {
@@ -1418,29 +1409,34 @@ main <- function() {
plot_configs <- list(
list(out_dir = out_dir_qc, filename = "L_vs_K_before_quality_control",
plot_configs = l_vs_k_plot_configs),
plot_configs = l_vs_k_plot_configs, page_width = 12, page_height = 8),
list(out_dir = out_dir_qc, filename = "frequency_delta_background",
plot_configs = frequency_delta_bg_plot_configs),
plot_configs = frequency_delta_bg_plot_configs, page_width = 12, page_height = 8),
list(out_dir = out_dir_qc, filename = "L_vs_K_above_threshold",
plot_configs = above_threshold_plot_configs),
plot_configs = above_threshold_plot_configs, page_width = 12, page_height = 8),
list(out_dir = out_dir_qc, filename = "plate_analysis",
plot_configs = plate_analysis_plot_configs),
plot_configs = plate_analysis_plot_configs, page_width = 14, page_height = 9),
list(out_dir = out_dir_qc, filename = "plate_analysis_boxplots",
plot_configs = plate_analysis_boxplot_configs),
plot_configs = plate_analysis_boxplot_configs, page_width = 18, page_height = 9),
list(out_dir = out_dir_qc, filename = "plate_analysis_no_zeros",
plot_configs = plate_analysis_no_zeros_plot_configs),
plot_configs = plate_analysis_no_zeros_plot_configs, page_width = 12, page_height = 8),
list(out_dir = out_dir_qc, filename = "plate_analysis_no_zeros_boxplots",
plot_configs = plate_analysis_no_zeros_boxplot_configs),
plot_configs = plate_analysis_no_zeros_boxplot_configs, page_width = 18, page_height = 9),
list(out_dir = out_dir_qc, filename = "L_vs_K_for_strains_2SD_outside_mean_K",
plot_configs = l_outside_2sd_k_plot_configs),
plot_configs = l_outside_2sd_k_plot_configs, page_width = 10, page_height = 8),
list(out_dir = out_dir_qc, filename = "delta_background_vs_K_for_strains_2SD_outside_mean_K",
plot_configs = delta_bg_outside_2sd_k_plot_configs)
plot_configs = delta_bg_outside_2sd_k_plot_configs, page_width = 10, page_height = 8)
)
# furrr::future_map(plot_configs, function(config) {
# generate_and_save_plots(config$out_dir, config$filename, config$plot_configs)
# }, .options = furrr_options(seed = TRUE))
# Parallelize background and quality control plot generation
furrr::future_map(plot_configs, function(config) {
generate_and_save_plots(config$out_dir, config$filename, config$plot_configs,
page_width = config$page_width, page_height = config$page_height)
}, .options = furrr_options(seed = TRUE))
# Loop over background strains
# TODO currently only tested against one strain, if we want to do multiple strains we'll
# have to rename or group the output files by dir or something so they don't get clobbered
bg_strains <- c("YDL227C")
lapply(bg_strains, function(strain) {
message("Processing background strain: ", strain)
@@ -1496,7 +1492,7 @@ main <- function() {
message("Generating reference interaction plots")
reference_plot_configs <- generate_interaction_plot_configs(df_interactions_reference_joined, "reference")
generate_and_save_plots(out_dir, "interaction_plots_reference", reference_plot_configs)
generate_and_save_plots(out_dir, "interaction_plots_reference", reference_plot_configs, page_width = 16, page_height = 16)
message("Setting missing deletion values to the highest theoretical value at each drug conc for L")
df_deletion <- df_na_stats %>% # formerly X2
@@ -1527,7 +1523,7 @@ main <- function() {
message("Generating deletion interaction plots")
deletion_plot_configs <- generate_interaction_plot_configs(df_interactions_joined, "deletion")
generate_and_save_plots(out_dir, "interaction_plots", deletion_plot_configs)
generate_and_save_plots(out_dir, "interaction_plots", deletion_plot_configs, page_width = 16, page_height = 16)
message("Writing enhancer/suppressor csv files")
interaction_threshold <- 2 # TODO add to study config?
@@ -1567,8 +1563,8 @@ main <- function() {
is_lm = FALSE,
adjust = TRUE
)
generate_and_save_plots(out_dir = out_dir, filename = "rank_plots",
plot_configs = rank_plot_configs)
generate_and_save_plots(out_dir, "rank_plots", rank_plot_configs,
page_width = 18, page_height = 12)
message("Generating ranked linear model plots")
rank_lm_plot_configs <- generate_rank_plot_configs(
@@ -1576,8 +1572,8 @@ main <- function() {
is_lm = TRUE,
adjust = TRUE
)
generate_and_save_plots(out_dir = out_dir, filename = "rank_plots_lm",
plot_configs = rank_lm_plot_configs)
generate_and_save_plots(out_dir, "rank_plots_lm", rank_lm_plot_configs,
page_width = 18, page_height = 12)
message("Generating filtered ranked plots")
rank_plot_filtered_configs <- generate_rank_plot_configs(
@@ -1586,10 +1582,8 @@ main <- function() {
adjust = FALSE,
overlap_color = TRUE
)
generate_and_save_plots(
out_dir = out_dir,
filename = "RankPlots_na_rm",
plot_configs = rank_plot_filtered_configs)
generate_and_save_plots(out_dir, "RankPlots_na_rm", rank_plot_filtered_configs,
page_width = 18, page_height = 12)
message("Generating filtered ranked linear model plots")
rank_plot_lm_filtered_configs <- generate_rank_plot_configs(
@@ -1598,20 +1592,15 @@ main <- function() {
adjust = FALSE,
overlap_color = TRUE
)
generate_and_save_plots(
out_dir = out_dir,
filename = "rank_plots_lm_na_rm",
plot_configs = rank_plot_lm_filtered_configs)
generate_and_save_plots(out_dir, "rank_plots_lm_na_rm", rank_plot_lm_filtered_configs,
page_width = 18, page_height = 12)
message("Generating correlation curve parameter pair plots")
correlation_plot_configs <- generate_correlation_plot_configs(
df_interactions_joined
)
generate_and_save_plots(
out_dir = out_dir,
filename = "correlation_cpps",
plot_configs = correlation_plot_configs,
)
generate_and_save_plots(out_dir, "correlation_cpps", correlation_plot_configs,
page_width = 10, page_height = 7)
})
})
}