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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( plot <- plot + geom_point(
shape = ifelse(!is.null(config$shape), config$shape, 3), shape = ifelse(!is.null(config$shape), config$shape, 3),
size = ifelse(!is.null(config$size), config$size, 1.5), 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 position = position
) )
@@ -807,14 +808,6 @@ generate_scatter_plot <- function(plot, config) {
# Extract necessary values # Extract necessary values
intercept <- config$lm_line$intercept # required intercept <- config$lm_line$intercept # required
slope <- config$lm_line$slope # 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]]))) 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]]))) 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") color <- ifelse(!is.null(config$lm_line$color), config$lm_line$color, "blue")
@@ -1542,30 +1535,30 @@ main <- function() {
plot_configs <- list( plot_configs <- list(
list(out_dir = out_dir_qc, filename = "L_vs_K_before_quality_control", 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), plot_configs = l_vs_k_plot_configs, page_width = 12, page_height = 8)
list(out_dir = out_dir_qc, filename = "frequency_delta_background", # list(out_dir = out_dir_qc, filename = "frequency_delta_background",
plot_configs = frequency_delta_bg_plot_configs, page_width = 12, page_height = 8), # 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", # list(out_dir = out_dir_qc, filename = "L_vs_K_above_threshold",
plot_configs = above_threshold_plot_configs, page_width = 12, page_height = 8), # plot_configs = above_threshold_plot_configs, page_width = 12, page_height = 8),
list(out_dir = out_dir_qc, filename = "plate_analysis", # list(out_dir = out_dir_qc, filename = "plate_analysis",
plot_configs = plate_analysis_plot_configs, page_width = 14, page_height = 9), # plot_configs = plate_analysis_plot_configs, page_width = 14, page_height = 9),
list(out_dir = out_dir_qc, filename = "plate_analysis_boxplots", # list(out_dir = out_dir_qc, filename = "plate_analysis_boxplots",
plot_configs = plate_analysis_boxplot_configs, page_width = 18, page_height = 9), # plot_configs = plate_analysis_boxplot_configs, page_width = 18, page_height = 9),
list(out_dir = out_dir_qc, filename = "plate_analysis_no_zeros", # 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), # 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", # 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), # 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", # 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), # 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", # 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 = delta_bg_outside_2sd_k_plot_configs, page_width = 10, page_height = 8)
) )
# Parallelize background and quality control plot generation # Parallelize background and quality control plot generation
# furrr::future_map(plot_configs, function(config) { furrr::future_map(plot_configs, function(config) {
# generate_and_save_plots(config$out_dir, config$filename, config$plot_configs, generate_and_save_plots(config$out_dir, config$filename, config$plot_configs,
# page_width = config$page_width, page_height = config$page_height) page_width = config$page_width, page_height = config$page_height)
# }, .options = furrr_options(seed = TRUE)) }, .options = furrr_options(seed = TRUE))
# Loop over background strains # Loop over background strains
# TODO currently only tested against one strain, if we want to do multiple strains we'll # 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(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) write.csv(interactions_reference_csv, file = file.path(out_dir, "zscore_interactions_reference.csv"), row.names = FALSE)
# message("Generating reference interaction plots") message("Generating reference interaction plots")
# reference_plot_configs <- generate_interaction_plot_configs(stats_reference, interactions_reference_joined, "reference") 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) 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") message("Setting missing deletion values to the highest theoretical value at each drug conc for L")
deletion_adjusted <- stats_na %>% # formerly X2 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(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) write.csv(interactions_csv, file = file.path(out_dir, "zscore_interactions.csv"), row.names = FALSE)
# message("Generating deletion interaction plots") message("Generating deletion interaction plots")
# deletion_plot_configs <- generate_interaction_plot_configs(stats_reference, interactions_joined, "deletion") 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) generate_and_save_plots(out_dir, "interaction_plots", deletion_plot_configs, page_width = 16, page_height = 16)
message("Writing enhancer/suppressor csv files") message("Writing enhancer/suppressor csv files")
interaction_threshold <- 2 # TODO add to study config? interaction_threshold <- 2 # TODO add to study config?