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Workaround buggy ggplot aes() implementation

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This commit is contained in:
Bryan Roessler
2024-10-08 14:30:33 -04:00
parent bff7e7cfb4
commit 96b7ec1fa1
1 changed files with 29 additions and 36 deletions
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65
qhtcp-workflow/apps/r/calculate_interaction_zscores.R
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@@ -717,7 +717,8 @@ generate_scatter_plot <- function(plot, config) {
plot <- plot + geom_point(
shape = ifelse(!is.null(config$shape), config$shape, 3),
size = ifelse(!is.null(config$size), config$size, 1.5),
color = ifelse(!is.null(config$color), config$color, "black"),
# Do not uncomment, something is broken in ggplot aes() even if this makes logical sense
# color = ifelse(!is.null(config$color), config$color, "black"),
position = position
)
@@ -807,14 +808,6 @@ generate_scatter_plot <- function(plot, config) {
# Extract necessary values
intercept <- config$lm_line$intercept # required
slope <- config$lm_line$slope # required
message("----- Generating lm_line -----")
message("Intercept: ", intercept)
message("Slope: ", slope)
message("Class: ", class(config$df[[config$x_var]]))
message("------------------------------")
xmin <- ifelse(!is.null(config$lm_line$xmin), config$lm_line$xmin, min(as.numeric(config$df[[config$x_var]])))
xmax <- ifelse(!is.null(config$lm_line$xmax), config$lm_line$xmax, max(as.numeric(config$df[[config$x_var]])))
color <- ifelse(!is.null(config$lm_line$color), config$lm_line$color, "blue")
@@ -1542,30 +1535,30 @@ 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, page_width = 12, page_height = 8),
list(out_dir = out_dir_qc, filename = "frequency_delta_background",
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, page_width = 12, page_height = 8),
list(out_dir = out_dir_qc, filename = "plate_analysis",
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, 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, page_width = 14, page_height = 9),
list(out_dir = out_dir_qc, filename = "plate_analysis_no_zeros_boxplots",
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, 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, page_width = 10, page_height = 8)
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, page_width = 12, page_height = 8),
# list(out_dir = out_dir_qc, filename = "L_vs_K_above_threshold",
# 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, page_width = 14, page_height = 9),
# list(out_dir = out_dir_qc, filename = "plate_analysis_boxplots",
# 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, page_width = 14, page_height = 9),
# list(out_dir = out_dir_qc, filename = "plate_analysis_no_zeros_boxplots",
# 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, 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, page_width = 10, page_height = 8)
)
# 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$page_height)
# }, .options = furrr_options(seed = TRUE))
furrr::future_map(plot_configs, function(config) {
generate_and_save_plots(config$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
@@ -1646,9 +1639,9 @@ main <- function() {
write.csv(calculations_reference_csv, file = file.path(out_dir, "zscore_calculations_reference.csv"), row.names = FALSE)
write.csv(interactions_reference_csv, file = file.path(out_dir, "zscore_interactions_reference.csv"), row.names = FALSE)
# message("Generating reference interaction plots")
# reference_plot_configs <- generate_interaction_plot_configs(stats_reference, interactions_reference_joined, "reference")
# generate_and_save_plots(out_dir, "interaction_plots_reference", reference_plot_configs, page_width = 16, page_height = 16)
message("Generating reference interaction plots")
reference_plot_configs <- generate_interaction_plot_configs(stats_reference, interactions_reference_joined, "reference")
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")
deletion_adjusted <- stats_na %>% # formerly X2
@@ -1679,9 +1672,9 @@ main <- function() {
write.csv(calculations_csv, file = file.path(out_dir, "zscore_calculations.csv"), row.names = FALSE)
write.csv(interactions_csv, file = file.path(out_dir, "zscore_interactions.csv"), row.names = FALSE)
# message("Generating deletion interaction plots")
# deletion_plot_configs <- generate_interaction_plot_configs(stats_reference, interactions_joined, "deletion")
# generate_and_save_plots(out_dir, "interaction_plots", deletion_plot_configs, page_width = 16, page_height = 16)
message("Generating deletion interaction plots")
deletion_plot_configs <- generate_interaction_plot_configs(stats_reference, interactions_joined, "deletion")
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?