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Skip nullgrob() since plot generation provides full chunks

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This commit is contained in:
Bryan Roessler
2024-10-06 18:16:16 -04:00
parent c6fec56630
commit bc0a7579c8
1 changed files with 29 additions and 38 deletions
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23
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) grid_layout$nrow <- ceiling(num_plots / grid_layout$ncol)
} }
total_spots <- grid_layout$nrow * grid_layout$ncol # total_spots <- grid_layout$nrow * grid_layout$ncol
num_plots <- length(static_plots) # num_plots <- length(static_plots)
if (num_plots < total_spots) { # if (num_plots < total_spots) {
message("Filling ", total_spots - num_plots, " empty spots with nullGrob()") # message("Filling ", total_spots - num_plots, " empty spots with nullGrob()")
static_plots <- c(static_plots, replicate(total_spots - num_plots, nullGrob(), simplify = FALSE)) # static_plots <- c(static_plots, replicate(total_spots - num_plots, nullGrob(), simplify = FALSE))
} # }
grid.arrange( grid.arrange(
grobs = static_plots, grobs = static_plots,
@@ -739,9 +739,6 @@ generate_scatter_plot <- function(plot, config) {
slope <- config$lm_line$slope slope <- config$lm_line$slope
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")
linewidth <- ifelse(!is.null(config$lm_line$linewidth), config$lm_line$linewidth, 1) linewidth <- ifelse(!is.null(config$lm_line$linewidth), config$lm_line$linewidth, 1)
# 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_min <- intercept + slope * x_min
y_max <- intercept + slope * x_max y_max <- intercept + slope * x_max
@@ -752,8 +749,6 @@ generate_scatter_plot <- function(plot, config) {
# Adjust or skip based on whether the values fall within limits # Adjust or skip based on whether the values fall within limits
if (y_min_within_limits && y_max_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( plot <- plot + annotate(
"segment", "segment",
x = x_min, x = x_min,
@@ -763,7 +758,6 @@ generate_scatter_plot <- function(plot, config) {
color = color, color = color,
linewidth = linewidth linewidth = linewidth
) )
}
} else { } else {
message("Skipping linear regression line due to y-values outside of limits") message("Skipping linear regression line due to y-values outside of limits")
} }
@@ -779,9 +773,6 @@ generate_scatter_plot <- function(plot, config) {
linewidth = linewidth linewidth = linewidth
) )
} }
} else {
message("Skipping linear regression line due to missing or invalid values")
}
} }
# Add SD Bands if specified # Add SD Bands if specified
@@ -1485,7 +1476,7 @@ main <- function() {
message("Generating quality control plots in parallel") message("Generating quality control plots in parallel")
# future::plan(future::multicore, workers = parallel::detectCores()) # 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( 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",