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Skip nullgrob() since plot generation provides full chunks

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Bryan Roessler
2024-10-06 18:16:16 -04:00
parent c6fec56630
commit bc0a7579c8
1 ha cambiato i file con 29 aggiunte e 38 eliminazioni
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67
qhtcp-workflow/apps/r/calculate_interaction_zscores.R
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@@ -597,13 +597,13 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs, page_width
grid_layout$nrow <- ceiling(num_plots / grid_layout$ncol)
}
total_spots <- grid_layout$nrow * grid_layout$ncol
num_plots <- length(static_plots)
# total_spots <- grid_layout$nrow * grid_layout$ncol
# num_plots <- length(static_plots)
if (num_plots < total_spots) {
message("Filling ", total_spots - num_plots, " empty spots with nullGrob()")
static_plots <- c(static_plots, replicate(total_spots - num_plots, nullGrob(), simplify = FALSE))
}
# if (num_plots < total_spots) {
# message("Filling ", total_spots - num_plots, " empty spots with nullGrob()")
# static_plots <- c(static_plots, replicate(total_spots - num_plots, nullGrob(), simplify = FALSE))
# }
grid.arrange(
grobs = static_plots,
@@ -739,36 +739,16 @@ generate_scatter_plot <- function(plot, config) {
slope <- config$lm_line$slope
color <- ifelse(!is.null(config$lm_line$color), config$lm_line$color, "blue")
linewidth <- ifelse(!is.null(config$lm_line$linewidth), config$lm_line$linewidth, 1)
y_min <- intercept + slope * x_min
y_max <- intercept + slope * x_max
# Ensure y-values are within y-limits (if any)
if (!is.null(config$ylim_vals)) {
y_min_within_limits <- y_min >= config$ylim_vals[1] && y_min <= config$ylim_vals[2]
y_max_within_limits <- y_max >= config$ylim_vals[1] && y_max <= config$ylim_vals[2]
# Ensure none of the values are NA and calculate y-values
if (!is.na(x_min) && !is.na(x_max) && !is.na(intercept) && !is.na(slope)) {
y_min <- intercept + slope * x_min
y_max <- intercept + slope * x_max
# Ensure y-values are within y-limits (if any)
if (!is.null(config$ylim_vals)) {
y_min_within_limits <- y_min >= config$ylim_vals[1] && y_min <= config$ylim_vals[2]
y_max_within_limits <- y_max >= config$ylim_vals[1] && y_max <= config$ylim_vals[2]
# Adjust or skip based on whether the values fall within limits
if (y_min_within_limits && y_max_within_limits) {
# Ensure x-values are also valid
if (!is.na(x_min) && !is.na(x_max)) {
plot <- plot + annotate(
"segment",
x = x_min,
xend = x_max,
y = y_min,
yend = y_max,
color = color,
linewidth = linewidth
)
}
} else {
message("Skipping linear regression line due to y-values outside of limits")
}
} else {
# If no y-limits are provided, proceed with the annotation
# Adjust or skip based on whether the values fall within limits
if (y_min_within_limits && y_max_within_limits) {
plot <- plot + annotate(
"segment",
x = x_min,
@@ -778,9 +758,20 @@ generate_scatter_plot <- function(plot, config) {
color = color,
linewidth = linewidth
)
} else {
message("Skipping linear regression line due to y-values outside of limits")
}
} else {
message("Skipping linear regression line due to missing or invalid values")
# If no y-limits are provided, proceed with the annotation
plot <- plot + annotate(
"segment",
x = x_min,
xend = x_max,
y = y_min,
yend = y_max,
color = color,
linewidth = linewidth
)
}
}
@@ -1052,7 +1043,7 @@ generate_interaction_plot_configs <- function(df_summary, df_interactions, type)
NG_value <- first(group_data_filtered$NG, default = 0)
DB_value <- first(group_data_filtered$DB, default = 0)
SM_value <- first(group_data_filtered$SM, default = 0)
lm_intercept_col <- paste0("lm_intercept_", var)
lm_slope_col <- paste0("lm_slope_", var)
lm_intercept_value <- first(group_data_filtered[[lm_intercept_col]], default = 0)
@@ -1485,7 +1476,7 @@ main <- function() {
message("Generating quality control plots in parallel")
# future::plan(future::multicore, workers = parallel::detectCores())
future::plan(future::multisession, workers = 3) # generate 3 plots in parallel
future::plan(future::multisession, workers = 3) # generate 3 plot files in parallel
plot_configs <- list(
list(out_dir = out_dir_qc, filename = "L_vs_K_before_quality_control",