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Break plate analysis out of main()

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This commit is contained in:
Bryan Roessler
2024-09-17 16:15:35 -04:00
parent 2ddba41950
commit 62cf10860a
1 changed files with 77 additions and 110 deletions
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187
qhtcp-workflow/apps/r/calculate_interaction_zscores.R
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@@ -355,7 +355,7 @@ calculate_interaction_scores <- function(df, max_conc, variables, group_vars) {
calculations_joined = calculations_joined)) calculations_joined = calculations_joined))
} }
generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_layout = NULL) { generate_and_save_plots <- function(out_dir, file_name, plot_configs, grid_layout = NULL) {
message("Generating ", file_name, ".pdf and ", file_name, ".html") message("Generating ", file_name, ".pdf and ", file_name, ".html")
# Prepare lists to collect plots # Prepare lists to collect plots
@@ -410,19 +410,9 @@ generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_la
} }
# Add interactive tooltips for plotly plots # Add interactive tooltips for plotly plots
tooltip_vars <- c("x", "y") tooltip_vars <- c()
if (!is.null(config$tooltip_vars)) { if (config$plot_type == "scatter") {
tooltip_vars <- config$tooltip_vars tooltip_vars <- c(config$x_var, config$y_var)
} else {
# Include default variables based on config
if (!is.null(config$delta_bg_point) && config$delta_bg_point) {
tooltip_vars <- c(tooltip_vars, "OrfRep", "Gene", "delta_bg")
} else if (!is.null(config$gene_point) && config$gene_point) {
tooltip_vars <- c(tooltip_vars, "OrfRep", "Gene")
} else {
# Include x and y variables by default
tooltip_vars <- c("x", "y")
}
} }
# Convert to plotly object # Convert to plotly object
@@ -437,7 +427,7 @@ generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_la
} }
# Save static PDF plots # Save static PDF plots
pdf(file.path(output_dir, paste0(file_name, ".pdf")), width = 14, height = 9) pdf(file.path(out_dir, paste0(file_name, ".pdf")), width = 14, height = 9)
lapply(static_plots, print) lapply(static_plots, print)
dev.off() dev.off()
@@ -445,16 +435,11 @@ generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_la
combined_plot <- subplot(plotly_plots, combined_plot <- subplot(plotly_plots,
nrows = ifelse(is.null(grid_layout$nrow), length(plotly_plots), grid_layout$nrow), nrows = ifelse(is.null(grid_layout$nrow), length(plotly_plots), grid_layout$nrow),
margin = 0.05) margin = 0.05)
saveWidget(combined_plot, file = file.path(output_dir, paste0(file_name, ".html")), selfcontained = TRUE) saveWidget(combined_plot, file = file.path(out_dir, paste0(file_name, ".html")), selfcontained = TRUE)
} }
generate_scatter_plot <- function(plot, config) { generate_scatter_plot <- function(plot, config) {
# Build the aes mapping with color if specified
if (!is.null(config$color_var)) {
plot <- plot + aes(color = .data[[config$color_var]])
}
# Determine Shape, Size, and Position for geom_point # Determine Shape, Size, and Position for geom_point
shape <- if (!is.null(config$shape)) config$shape else 3 shape <- if (!is.null(config$shape)) config$shape else 3
size <- if (!is.null(config$size)) config$size else 0.1 size <- if (!is.null(config$size)) config$size else 0.1
@@ -462,7 +447,6 @@ generate_scatter_plot <- function(plot, config) {
# Add geom_point with determined parameters # Add geom_point with determined parameters
plot <- plot + geom_point( plot <- plot + geom_point(
aes(color = .data[[config$color_var]]),
shape = shape, shape = shape,
size = size, size = size,
position = position position = position
@@ -470,7 +454,6 @@ generate_scatter_plot <- function(plot, config) {
if (!is.null(config$cyan_points)) { if (!is.null(config$cyan_points)) {
plot <- plot + geom_point( plot <- plot + geom_point(
data = subset(config$df, is_cyan_point == TRUE),
aes(x = .data[[config$x_var]], y = .data[[config$y_var]]), aes(x = .data[[config$x_var]], y = .data[[config$y_var]]),
color = "cyan", color = "cyan",
shape = 3, shape = 3,
@@ -618,6 +601,38 @@ generate_box_plot <- function(plot, config) {
return(plot) return(plot)
} }
generate_plate_analysis_plot_configs <- function(variables, stages = c("before", "after"),
df_before = NULL, df_after = NULL, plot_type = "scatter") {
plots <- list()
for (var in variables) {
for (stage in stages) {
df_plot <- if (stage == "before") df_before else df_after
# Adjust settings based on plot_type
if (plot_type == "scatter") {
error_bar <- TRUE
position <- "jitter"
} else if (plot_type == "box") {
error_bar <- FALSE
position <- NULL
}
config <- list(
df = df_plot,
x_var = "scan",
y_var = var,
plot_type = plot_type,
title = paste("Plate analysis by Drug Conc for", var, stage, "quality control"),
error_bar = error_bar,
color_var = "conc_num_factor",
position = position
)
plots <- append(plots, list(config))
}
}
return(plots)
}
generate_interaction_plot_configs <- function(df, variables) { generate_interaction_plot_configs <- function(df, variables) {
configs <- list() configs <- list()
@@ -842,7 +857,7 @@ generate_rank_plot_configs <- function(df_filtered, variables, is_lm = FALSE) {
color_var = "Overlap", color_var = "Overlap",
x_label = x_var, x_label = x_var,
y_label = y_var, y_label = y_var,
rectangles = rectangles # Add rectangles configuration rectangles = rectangles
) )
} }
} }
@@ -871,7 +886,7 @@ generate_correlation_plot_configs <- function(df) {
config <- list( config <- list(
df = df, df = df,
x_var = rel$x, x_var = rel$x,
y_var = rel.y, y_var = rel$y,
plot_type = "scatter", plot_type = "scatter",
title = rel$label, title = rel$label,
x_label = paste("z-score", gsub("Z_lm_", "", rel$x)), x_label = paste("z-score", gsub("Z_lm_", "", rel$x)),
@@ -1137,79 +1152,31 @@ main <- function() {
) )
) )
plate_analysis_plots <- list() plate_analysis_plot_configs <- generate_plate_analysis_plot_configs(
for (var in summary_vars) { variables = summary_vars,
for (stage in c("before", "after")) { df_before = df_filtered_stats,
if (stage == "before") { df_after = df_na_filtered_stats,
df_plot <- df_filtered_stats )
} else {
df_plot <- df_na_filtered_stats
}
config <- list(
df = df_plot,
x_var = "scan",
y_var = var,
plot_type = "scatter",
title = paste("Plate analysis by Drug Conc for", var, stage, "quality control"),
error_bar = TRUE,
color_var = "conc_num_factor",
position = "jitter")
plate_analysis_plots <- append(plate_analysis_plots, list(config)) plate_analysis_box_plot_configs <- generate_plate_analysis_plot_configs(
} variables = summary_vars,
} df_before = df_filtered_stats,
df_after = df_na_filtered_stats,
plot_type = "box"
)
plate_analysis_boxplots <- list() plate_analysis_no_zeros_plot_configs <- generate_plate_analysis_plot_configs(
for (var in summary_vars) { variables = summary_vars,
for (stage in c("before", "after")) { stages = c("after"), # Only after QC
if (stage == "before") { df_after = df_no_zeros_filtered_stats,
df_plot <- df_filtered_stats )
} else {
df_plot <- df_na_filtered_stats
}
config <- list(
df = df_plot,
x_var = "scan",
y_var = var,
plot_type = "box",
title = paste("Plate analysis by Drug Conc for", var, stage, "quality control"),
error_bar = FALSE,
color_var = "conc_num_factor")
plate_analysis_boxplots <- append(plate_analysis_boxplots, list(config)) plate_analysis_no_zeros_boxplot_configs <- generate_plate_analysis_plot_configs(
} variables = summary_vars,
} stages = c("after"), # Only after QC
df_after = df_no_zeros_filtered_stats,
plate_analysis_no_zeros_plots <- list() plot_type = "box"
for (var in summary_vars) { )
config <- list(
df = df_no_zeros_filtered_stats,
x_var = "scan",
y_var = var,
plot_type = "scatter",
title = paste("Plate analysis by Drug Conc for", var, "after quality control"),
error_bar = TRUE,
color_var = "conc_num_factor",
position = "jitter")
plate_analysis_no_zeros_plots <- append(plate_analysis_no_zeros_plots, list(config))
}
plate_analysis_no_zeros_boxplots <- list()
for (var in summary_vars) {
config <- list(
df = df_no_zeros_filtered_stats,
x_var = "scan",
y_var = var,
plot_type = "box",
title = paste("Plate analysis by Drug Conc for", var, "after quality control"),
error_bar = FALSE,
color_var = "conc_num_factor"
)
plate_analysis_no_zeros_boxplots <- append(plate_analysis_no_zeros_boxplots, list(config))
}
l_outside_2sd_k_plots <- list( l_outside_2sd_k_plots <- list(
list( list(
@@ -1239,16 +1206,16 @@ main <- function() {
) )
) )
# message("Generating quality control 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, "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, "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, "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", plate_analysis_plot_configs)
# generate_and_save_plots(out_dir_qc, "plate_analysis_boxplots", plate_analysis_boxplots) 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_plots) 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_boxplots) 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, "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) 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 # Process background strains
bg_strains <- c("YDL227C") bg_strains <- c("YDL227C")
@@ -1399,7 +1366,7 @@ main <- function() {
variables = interaction_vars, variables = interaction_vars,
is_lm = FALSE is_lm = FALSE
) )
generate_and_save_plots(output_dir = out_dir, file_name = "RankPlots", generate_and_save_plots(out_dir = out_dir, file_name = "RankPlots",
plot_configs = rank_plot_configs, grid_layout = list(ncol = 3, nrow = 2)) plot_configs = rank_plot_configs, grid_layout = list(ncol = 3, nrow = 2))
message("Generating ranked linear model plots") message("Generating ranked linear model plots")
@@ -1408,7 +1375,7 @@ main <- function() {
variables = interaction_vars, variables = interaction_vars,
is_lm = TRUE is_lm = TRUE
) )
generate_and_save_plots(output_dir = out_dir, file_name = "RankPlots_lm", generate_and_save_plots(out_dir = out_dir, file_name = "RankPlots_lm",
plot_configs = rank_lm_plot_configs, grid_layout = list(ncol = 3, nrow = 2)) plot_configs = rank_lm_plot_configs, grid_layout = list(ncol = 3, nrow = 2))
message("Filtering and reranking plots") message("Filtering and reranking plots")
@@ -1449,7 +1416,7 @@ main <- function() {
message("Generating filtered ranked plots") message("Generating filtered ranked plots")
generate_and_save_plots( generate_and_save_plots(
output_dir = out_dir, out_dir = out_dir,
file_name = "RankPlots_na_rm", file_name = "RankPlots_na_rm",
plot_configs = rank_plot_filtered_configs, plot_configs = rank_plot_filtered_configs,
grid_layout = list(ncol = 3, nrow = 2)) grid_layout = list(ncol = 3, nrow = 2))
@@ -1461,7 +1428,7 @@ main <- function() {
is_lm = TRUE is_lm = TRUE
) )
generate_and_save_plots( generate_and_save_plots(
output_dir = out_dir, out_dir = out_dir,
file_name = "RankPlots_lm_na_rm", file_name = "RankPlots_lm_na_rm",
plot_configs = rank_plot_lm_filtered_configs, plot_configs = rank_plot_lm_filtered_configs,
grid_layout = list(ncol = 3, nrow = 2)) grid_layout = list(ncol = 3, nrow = 2))
@@ -1469,7 +1436,7 @@ main <- function() {
message("Generating correlation plots") message("Generating correlation plots")
correlation_plot_configs <- generate_correlation_plot_configs(zscores_interactions_filtered) correlation_plot_configs <- generate_correlation_plot_configs(zscores_interactions_filtered)
generate_and_save_plots( generate_and_save_plots(
output_dir = out_dir, out_dir = out_dir,
file_name = "Avg_Zscore_vs_lm_NA_rm", file_name = "Avg_Zscore_vs_lm_NA_rm",
plot_configs = correlation_plot_configs, plot_configs = correlation_plot_configs,
grid_layout = list(ncol = 2, nrow = 2)) grid_layout = list(ncol = 2, nrow = 2))