From 54c4af8bf7965c006ac9c36d986cd204fd52e001 Mon Sep 17 00:00:00 2001
From: rrbutler <6644896+rbutleriii@users.noreply.github.com>
Date: Wed, 28 May 2025 16:47:38 -0700
Subject: [PATCH 01/15] Updating plot ggrepel

---
 R/bootstrap_plot.R | 24 +++++++++++++++---------
 1 file changed, 15 insertions(+), 9 deletions(-)

diff --git a/R/bootstrap_plot.R b/R/bootstrap_plot.R
index 702301b..23d4853 100755
--- a/R/bootstrap_plot.R
+++ b/R/bootstrap_plot.R
@@ -27,6 +27,7 @@ bootstrap_plot <- function(gene_data,
     
     requireNamespace("ggplot2")
     requireNamespace("patchwork")
+    requireNamespace("ggrepel")
     Pos <- Rep <- Exp <- p <- significant <- CellType <- NULL;
     
     exp_mats_msg <- paste(
@@ -36,8 +37,7 @@ bootstrap_plot <- function(gene_data,
     plots <- list()
     #### Set up save path ####
     dir.create(save_dir, showWarnings = FALSE, recursive = TRUE)  
-    gene_data$symLab <- ifelse(gene_data$hit > 25, 
-                               sprintf("  %s", gene_data$gene), NA) 
+    gene_data$symLab <- ifelse(gene_data$hit > 25, gene_data$gene, "") 
     
     #### Filter gene_data ####
     if(!is.null(signif_ct)){
@@ -70,7 +70,7 @@ bootstrap_plot <- function(gene_data,
         facet_grid(facets = facets, 
                    scales = scales) + 
         add_line() +
-        theme_graph() 
+        theme_classic() 
     plots[["plot1"]] <- g1 
     messager("Saving plot -->", files[[1]], v=verbose)
     ggplot2::ggsave(filename = files[[1]], 
@@ -80,12 +80,18 @@ bootstrap_plot <- function(gene_data,
     
     #### Plot 2: Plot with gene names  ####
     g2 <- g1 + 
-        geom_text(aes_string(label = "symLab"),
-                   # fill=ggplot2::alpha("black",.5),
-                   color=ggplot2::alpha("black",.75),
-                   na.rm = TRUE,
-                  hjust = 0, vjust = 0, size = 3
-        ) + 
+        geom_text_repel(
+          mapping = aes(label = symLab), 
+          alpha = 0.75,
+          segment.alpha = 0.75,
+          max.overlaps = 15
+        ) +
+        # geom_text(aes_string(label = "symLab"),
+                   # # fill=ggplot2::alpha("black",.5),
+                   # color=ggplot2::alpha("black",.75),
+                   # na.rm = TRUE,
+                  # hjust = 0, vjust = 0, size = 3
+        # ) + 
         scale_x_discrete(expand = expansion(mult = c(0,.15))) +
         scale_y_discrete(expand = expansion(mult = c(0,.15))) 
     plots[["plot2"]] <- g2 

From 61d993e2c1647f97ff1322c4240dbc9da052ce40 Mon Sep 17 00:00:00 2001
From: rrbutler <6644896+rbutleriii@users.noreply.github.com>
Date: Wed, 28 May 2025 17:10:23 -0700
Subject: [PATCH 02/15] Changing abline, file widths

---
 R/bootstrap_plot.R | 47 +++++++++++++++++++++++-----------------------
 1 file changed, 24 insertions(+), 23 deletions(-)

diff --git a/R/bootstrap_plot.R b/R/bootstrap_plot.R
index 23d4853..6e067ba 100755
--- a/R/bootstrap_plot.R
+++ b/R/bootstrap_plot.R
@@ -56,27 +56,31 @@ bootstrap_plot <- function(gene_data,
     }
     ## Plot several variants of the graph ##
     add_line <- function(){
-        geom_abline(intercept = 0, slope = 1, 
-                    linetype = "dashed",
-                    colour = ggplot2::alpha("red",.5)) 
+      geom_abline(
+        intercept = 0, 
+        slope = 1, 
+        linetype = "dashed",
+        color = "red", 
+        alpha = 0.5
+      ) 
     } 
     #### Plot 1: Plot without gene names  ####
-    g1 <- ggplot(gene_data,
-                          aes_string(x = "boot", y = "hit",  color="hit")) +
-        geom_point(size = 1,  alpha=.75) + 
+    g1 <- ggplot(gene_data, aes(x = boot, y = hit,  color = hit)) +
+        geom_point(size = 1,  alpha = .75) + 
         xlab("Mean Bootstrap Expression") +
         ylab("Expression in cell type (%)\n") +
         scale_color_viridis_c() +
-        facet_grid(facets = facets, 
-                   scales = scales) + 
+        facet_grid(facets = facets, scales = scales) + 
         add_line() +
         theme_classic() 
     plots[["plot1"]] <- g1 
     messager("Saving plot -->", files[[1]], v=verbose)
-    ggplot2::ggsave(filename = files[[1]], 
-                    plot = g1,
-                    width = 3.5, 
-                    height = 3.5) 
+    ggsave(
+      filename = files[[1]], 
+      plot = g1,
+      width = 4, 
+      height = 3.5
+    )
     
     #### Plot 2: Plot with gene names  ####
     g2 <- g1 + 
@@ -84,22 +88,19 @@ bootstrap_plot <- function(gene_data,
           mapping = aes(label = symLab), 
           alpha = 0.75,
           segment.alpha = 0.75,
-          max.overlaps = 15
+          max.overlaps = 25,
+          force_pull = 0.5
         ) +
-        # geom_text(aes_string(label = "symLab"),
-                   # # fill=ggplot2::alpha("black",.5),
-                   # color=ggplot2::alpha("black",.75),
-                   # na.rm = TRUE,
-                  # hjust = 0, vjust = 0, size = 3
-        # ) + 
         scale_x_discrete(expand = expansion(mult = c(0,.15))) +
         scale_y_discrete(expand = expansion(mult = c(0,.15))) 
     plots[["plot2"]] <- g2 
     messager("Saving plot -->", files[[2]], v=verbose)
-    ggplot2::ggsave(filename = files[[2]], 
-                    plot = g2,
-                    width = 3.5, 
-                    height = 3.5) 
+    ggsave(
+      filename = files[[2]], 
+      plot = g2,
+      width = 4, 
+      height = 3.5
+    ) 
    
  
     #### Plot 3 ####

From 2b38f542f97bd9f19abc0feedc6d6afa16ffe8eb Mon Sep 17 00:00:00 2001
From: rrbutler <6644896+rbutleriii@users.noreply.github.com>
Date: Wed, 28 May 2025 17:22:02 -0700
Subject: [PATCH 03/15] file widths

---
 R/bootstrap_plot.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/R/bootstrap_plot.R b/R/bootstrap_plot.R
index 6e067ba..9b26b9f 100755
--- a/R/bootstrap_plot.R
+++ b/R/bootstrap_plot.R
@@ -141,11 +141,12 @@ bootstrap_plot <- function(gene_data,
             scale_x_discrete(breaks = NULL) +
             theme_graph() +
             facet_wrap(facets=facets)
+        wd <- 1 + length(unique(melt_boot[, hit])) * 0.25 
         plots[["plot3"]] <- g3
         messager("Saving plot -->", files[[3]], v=verbose)
         ggplot2::ggsave(filename = files[[3]], 
                         plot = g3,
-                        width = 3.5, 
+                        width = wd, 
                         height = 3.5) 
         
         
@@ -189,7 +190,7 @@ bootstrap_plot <- function(gene_data,
             labs(x=expression("Least specific" %->% "Most specific"),
                  y="Expression in cell type (%)\n") 
         #### Save ####
-        wd <- 1 + length(unique(melt_boot[,4])) * 0.175 
+        wd <- 1 + length(unique(melt_boot[,4])) * 0.25 
         plots[["plot4"]] <- g4
         messager("Saving plot -->", files[[4]], v=verbose)
         ggplot2::ggsave(filename = files[[4]], 

From 67ca405ef3a47691d045b32e52939e9134e3ed89 Mon Sep 17 00:00:00 2001
From: rrbutler <6644896+rbutleriii@users.noreply.github.com>
Date: Wed, 28 May 2025 17:52:52 -0700
Subject: [PATCH 04/15] file widths

---
 R/bootstrap_plot.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/R/bootstrap_plot.R b/R/bootstrap_plot.R
index 9b26b9f..15e4202 100755
--- a/R/bootstrap_plot.R
+++ b/R/bootstrap_plot.R
@@ -91,8 +91,8 @@ bootstrap_plot <- function(gene_data,
           max.overlaps = 25,
           force_pull = 0.5
         ) +
-        scale_x_discrete(expand = expansion(mult = c(0,.15))) +
-        scale_y_discrete(expand = expansion(mult = c(0,.15))) 
+        # scale_x_discrete(expand = expansion(mult = c(0,.15))) +
+        # scale_y_discrete(expand = expansion(mult = c(0,.15))) 
     plots[["plot2"]] <- g2 
     messager("Saving plot -->", files[[2]], v=verbose)
     ggsave(
@@ -141,6 +141,7 @@ bootstrap_plot <- function(gene_data,
             scale_x_discrete(breaks = NULL) +
             theme_graph() +
             facet_wrap(facets=facets)
+        print(sprintf("Names of melt boot: %s", paste(names(melt_boot), collapse = " ")))
         wd <- 1 + length(unique(melt_boot[, hit])) * 0.25 
         plots[["plot3"]] <- g3
         messager("Saving plot -->", files[[3]], v=verbose)

From ee23df226acb4f8c4f0614ef2b39a39e7f14591b Mon Sep 17 00:00:00 2001
From: rrbutler <6644896+rbutleriii@users.noreply.github.com>
Date: Wed, 28 May 2025 18:01:31 -0700
Subject: [PATCH 05/15] issue with plot

---
 R/bootstrap_plot.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/bootstrap_plot.R b/R/bootstrap_plot.R
index 15e4202..e22fd7a 100755
--- a/R/bootstrap_plot.R
+++ b/R/bootstrap_plot.R
@@ -90,7 +90,7 @@ bootstrap_plot <- function(gene_data,
           segment.alpha = 0.75,
           max.overlaps = 25,
           force_pull = 0.5
-        ) +
+        ) # +
         # scale_x_discrete(expand = expansion(mult = c(0,.15))) +
         # scale_y_discrete(expand = expansion(mult = c(0,.15))) 
     plots[["plot2"]] <- g2 

From b533c60017de7784181208a1ab16d9fdfc07564a Mon Sep 17 00:00:00 2001
From: rrbutler <6644896+rbutleriii@users.noreply.github.com>
Date: Wed, 28 May 2025 18:15:35 -0700
Subject: [PATCH 06/15] flip colors, say melt_boot names

---
 R/bootstrap_plot.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/bootstrap_plot.R b/R/bootstrap_plot.R
index e22fd7a..d9ca740 100755
--- a/R/bootstrap_plot.R
+++ b/R/bootstrap_plot.R
@@ -69,7 +69,7 @@ bootstrap_plot <- function(gene_data,
         geom_point(size = 1,  alpha = .75) + 
         xlab("Mean Bootstrap Expression") +
         ylab("Expression in cell type (%)\n") +
-        scale_color_viridis_c() +
+        scale_color_viridis_c(direction = -1) +
         facet_grid(facets = facets, scales = scales) + 
         add_line() +
         theme_classic() 
@@ -141,7 +141,7 @@ bootstrap_plot <- function(gene_data,
             scale_x_discrete(breaks = NULL) +
             theme_graph() +
             facet_wrap(facets=facets)
-        print(sprintf("Names of melt boot: %s", paste(names(melt_boot), collapse = " ")))
+        cat("Names of melt boot:", paste(names(melt_boot), collapse = " "))
         wd <- 1 + length(unique(melt_boot[, hit])) * 0.25 
         plots[["plot3"]] <- g3
         messager("Saving plot -->", files[[3]], v=verbose)

From 181e60481f6c09d8d379fc8cbe0e3acdd9cabb03 Mon Sep 17 00:00:00 2001
From: rrbutler <6644896+rbutleriii@users.noreply.github.com>
Date: Wed, 28 May 2025 18:28:46 -0700
Subject: [PATCH 07/15] unclear error melt_boot names

---
 R/bootstrap_plot.R | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/R/bootstrap_plot.R b/R/bootstrap_plot.R
index d9ca740..8372102 100755
--- a/R/bootstrap_plot.R
+++ b/R/bootstrap_plot.R
@@ -141,13 +141,13 @@ bootstrap_plot <- function(gene_data,
             scale_x_discrete(breaks = NULL) +
             theme_graph() +
             facet_wrap(facets=facets)
-        cat("Names of melt boot:", paste(names(melt_boot), collapse = " "))
-        wd <- 1 + length(unique(melt_boot[, hit])) * 0.25 
+        # cat("Names of melt boot:", paste(names(melt_boot), collapse = " "))
+        # wd <- 1 + length(unique(melt_boot[, hit])) * 0.25 
         plots[["plot3"]] <- g3
         messager("Saving plot -->", files[[3]], v=verbose)
         ggplot2::ggsave(filename = files[[3]], 
                         plot = g3,
-                        width = wd, 
+                        width = 8, 
                         height = 3.5) 
         
         
@@ -191,12 +191,12 @@ bootstrap_plot <- function(gene_data,
             labs(x=expression("Least specific" %->% "Most specific"),
                  y="Expression in cell type (%)\n") 
         #### Save ####
-        wd <- 1 + length(unique(melt_boot[,4])) * 0.25 
+        # wd <- 1 + length(unique(melt_boot[,4])) * 0.25 
         plots[["plot4"]] <- g4
         messager("Saving plot -->", files[[4]], v=verbose)
         ggplot2::ggsave(filename = files[[4]], 
                         plot = g4,
-                        width = wd, 
+                        width = 8,
                         height = 4) 
     }
    

From 12052e959abbf349666a86193a675f300d7bd8b8 Mon Sep 17 00:00:00 2001
From: rrbutler <6644896+rbutleriii@users.noreply.github.com>
Date: Fri, 19 Sep 2025 13:47:52 -0700
Subject: [PATCH 08/15] Checking #98

---
 R/check_full_results.R | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/R/check_full_results.R b/R/check_full_results.R
index af06975..cf61ff2 100755
--- a/R/check_full_results.R
+++ b/R/check_full_results.R
@@ -23,13 +23,9 @@ check_full_results <- function(full_results,
             " sct_data. Perhaps the wrong annotLevel was used?"
         )
         if (sum(!as.character(unique(full_results$results$CellType)) %in%
-            colnames(sct_data[[1]]$specificity)) ==
+            colnames(sct_data[[annotLevel]]$specificity)) ==
             length(as.character(unique(full_results$results$CellType)))) {
             stop(err_msg2)
         }
-        if (sum(!as.character(unique(full_results$results$CellType)) %in%
-            colnames(sct_data[[1]]$specificity)) > 0) {
-            stop(err_msg2)
-        }
     }
 }

From 45570cc9cfe77e738d186b9e7a869932654ff204 Mon Sep 17 00:00:00 2001
From: rrbutler <6644896+rbutleriii@users.noreply.github.com>
Date: Fri, 19 Sep 2025 14:11:21 -0700
Subject: [PATCH 09/15] specify annot #98

---
 R/check_full_results.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/check_full_results.R b/R/check_full_results.R
index cf61ff2..580e8fb 100755
--- a/R/check_full_results.R
+++ b/R/check_full_results.R
@@ -8,7 +8,8 @@
 #' 
 #' @keywords internal
 check_full_results <- function(full_results,
-                               sct_data) {
+                               sct_data,
+                               annotLevel = annotLevel) {
     if (!is.null(full_results)) {
         err_msg <- paste0(
             "ERROR: full_results must be a list of length 3 or 4",

From b6b1b34c60087b4b2e016423e434f6f62833ae26 Mon Sep 17 00:00:00 2001
From: rrbutler <6644896+rbutleriii@users.noreply.github.com>
Date: Fri, 19 Sep 2025 14:38:58 -0700
Subject: [PATCH 10/15] specify annot #98

---
 R/check_full_results.R       | 2 +-
 R/generate_bootstrap_plots.r | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/R/check_full_results.R b/R/check_full_results.R
index 580e8fb..15bbddc 100755
--- a/R/check_full_results.R
+++ b/R/check_full_results.R
@@ -9,7 +9,7 @@
 #' @keywords internal
 check_full_results <- function(full_results,
                                sct_data,
-                               annotLevel = annotLevel) {
+                               annotLevel) {
     if (!is.null(full_results)) {
         err_msg <- paste0(
             "ERROR: full_results must be a list of length 3 or 4",
diff --git a/R/generate_bootstrap_plots.r b/R/generate_bootstrap_plots.r
index 4cf3038..e97c8b1 100755
--- a/R/generate_bootstrap_plots.r
+++ b/R/generate_bootstrap_plots.r
@@ -153,7 +153,8 @@ generate_bootstrap_plots <- function(sct_data = NULL,
     )
     check_full_results(
         full_results = full_results,
-        sct_data = sct_data
+        sct_data = sct_data,
+        annotLevel = annotLevel
     ) 
     results <- full_results$results
     #### Check gene lists ####

From bb1f6cbd22d9f94036f4745feec1a801cac255f4 Mon Sep 17 00:00:00 2001
From: rrbutler <6644896+rbutleriii@users.noreply.github.com>
Date: Thu, 2 Oct 2025 16:42:03 -0700
Subject: [PATCH 11/15] split qqs to multiple pages

---
 R/bootstrap_plot.R | 164 +++++++++++++++++++++++++++++++++------------
 1 file changed, 121 insertions(+), 43 deletions(-)

diff --git a/R/bootstrap_plot.R b/R/bootstrap_plot.R
index 8372102..7a8d4bc 100755
--- a/R/bootstrap_plot.R
+++ b/R/bootstrap_plot.R
@@ -1,3 +1,110 @@
+#' Create a multi-page PDF with each cell type on a separate page
+#'
+#' This function creates a PDF where each unique value in a specified faceting 
+#' variable (typically "CellType") is plotted on a separate page. Each plot shows 
+#' expression data with points colored by expression levels.
+#'
+#' @param gene_data A data frame containing gene expression data with columns for 
+#'   "boot", "hit", and a faceting variable (typically "CellType").
+#' @param facet_var Character string specifying the column name to use for 
+#'   separating plots onto different pages (e.g., "CellType").
+#' @param output_file Character string specifying the path to save the PDF file.
+#' @param add_labels Character string specifying the column name to use for point labels,
+#'   or NULL to disable labels (default: NULL).
+#' @param verbose Logical indicating whether to print progress messages (default: TRUE).
+#'
+#' @return No return value, called for side effect of creating a PDF file.
+#'
+#' @details The function creates QQ plots of "boot" vs "hit" values, with points 
+#'   colored by "hit" values using a reversed viridis color scale. Each plot includes
+#'   a title showing the cell type being displayed. If add_labels is provided, text labels
+#'   from the specified column will be added to the points using ggrepel.
+#'
+#' @examples
+#' \dontrun{
+#' # Create plots without labels
+#' .create_multipage_plot(
+#'   gene_data = my_gene_data,
+#'   facet_var = "CellType",
+#'   output_file = "cell_type_plots.pdf"
+#' )
+#'
+#' # Create plots with gene symbol labels
+#' .create_multipage_plot(
+#'   gene_data = my_gene_data,
+#'   facet_var = "CellType",
+#'   output_file = "cell_type_plots_labeled.pdf",
+#'   add_labels = "gene_symbol"
+#' )
+#' }
+#'
+#' @import ggplot2
+#' @importFrom viridis scale_color_viridis_c
+#' @importFrom ggrepel geom_text_repel
+#'
+#' @keywords internal 
+.create_multipage_plot <- function(gene_data, facet_var, output_file, 
+                                   add_labels = NULL, verbose = TRUE) {
+  # Check for required packages
+  if(!is.null(add_labels) && !requireNamespace("ggrepel", quietly = TRUE)) {
+    stop("Package 'ggrepel' is needed for adding labels. Please install it.",
+         call. = FALSE)
+  }
+  
+  if (verbose) messager("Saving plot -->", output_file)
+  # Check if the specified label column exists
+  if(!is.null(add_labels) && !(add_labels %in% colnames(gene_data))) {
+    stop(paste0("Label column '", add_labels, "' not found in data."),
+         call. = FALSE)
+  }
+  
+  # Get unique cell types
+  cell_types <- unique(gene_data[[facet_var]])
+  
+  # Start PDF device
+  pdf(output_file, width = 7, height = 7)
+  
+  # Create and print a plot for each cell type
+  for (cell_type in cell_types) {
+    # Subset data for this cell type
+    subset_data <- gene_data[gene_data[[facet_var]] == cell_type, ]
+    
+    # Create base plot for this cell type
+    g <- ggplot(subset_data, aes(x = boot, y = hit, color = hit)) +
+      geom_point(size = 1, alpha = .75) + 
+      xlab("Mean Bootstrap Expression") +
+      ylab("Expression in cell type (%)\n") +
+      scale_color_viridis_c(direction = -1) +
+      ggtitle(paste("Cell Type:", cell_type)) +
+      add_line() +
+      theme_classic()
+    
+    # Add labels if a column name was provided
+    if(!is.null(add_labels)) {
+      g <- g + ggrepel::geom_text_repel(
+        aes(label = .data[[add_labels]]),  # Use the column name dynamically
+        size = 3,
+        box.padding = 0.35,
+        point.padding = 0.5,
+        segment.color = "grey50",
+        max.overlaps = 25
+      )
+      
+      if (verbose) messager("Added labels from column:", add_labels)
+    }
+    
+    # Print the plot (adds it to the PDF)
+    print(g)
+    
+    if (verbose) messager("Added plot for", cell_type)
+  }
+  
+  # Close the PDF device
+  dev.off()
+  
+}
+
+
 #' Bootstrap plot
 #' 
 #' Plot bootstrap enrichment results. 
@@ -55,53 +162,22 @@ bootstrap_plot <- function(gene_data,
         dir.create(dirname(f), showWarnings = FALSE, recursive = TRUE)   
     }
     ## Plot several variants of the graph ##
-    add_line <- function(){
-      geom_abline(
-        intercept = 0, 
-        slope = 1, 
-        linetype = "dashed",
-        color = "red", 
-        alpha = 0.5
-      ) 
-    } 
     #### Plot 1: Plot without gene names  ####
-    g1 <- ggplot(gene_data, aes(x = boot, y = hit,  color = hit)) +
-        geom_point(size = 1,  alpha = .75) + 
-        xlab("Mean Bootstrap Expression") +
-        ylab("Expression in cell type (%)\n") +
-        scale_color_viridis_c(direction = -1) +
-        facet_grid(facets = facets, scales = scales) + 
-        add_line() +
-        theme_classic() 
-    plots[["plot1"]] <- g1 
-    messager("Saving plot -->", files[[1]], v=verbose)
-    ggsave(
-      filename = files[[1]], 
-      plot = g1,
-      width = 4, 
-      height = 3.5
+    .create_multipage_plot(
+      gene_data = gene_data,
+      facet_var = "CellType",  # Column name containing cell types
+      output_file = files[[1]],
+      verbose = verbose
     )
     
     #### Plot 2: Plot with gene names  ####
-    g2 <- g1 + 
-        geom_text_repel(
-          mapping = aes(label = symLab), 
-          alpha = 0.75,
-          segment.alpha = 0.75,
-          max.overlaps = 25,
-          force_pull = 0.5
-        ) # +
-        # scale_x_discrete(expand = expansion(mult = c(0,.15))) +
-        # scale_y_discrete(expand = expansion(mult = c(0,.15))) 
-    plots[["plot2"]] <- g2 
-    messager("Saving plot -->", files[[2]], v=verbose)
-    ggsave(
-      filename = files[[2]], 
-      plot = g2,
-      width = 4, 
-      height = 3.5
-    ) 
-   
+    .create_multipage_plot(
+      gene_data = gene_data,
+      facet_var = "CellType",  # Column name containing cell types
+      output_file = files[[2]],
+      add_labels = "symLab",
+      verbose = verbose
+    )
  
     #### Plot 3 ####
     if(is.null(exp_mats)){
@@ -204,3 +280,5 @@ bootstrap_plot <- function(gene_data,
     return(list(plots=plots,
                 paths=files))
 }
+
+

From a0a996a622ee2f8f5d5ef0649c8466e20813857a Mon Sep 17 00:00:00 2001
From: rrbutler <6644896+rbutleriii@users.noreply.github.com>
Date: Thu, 2 Oct 2025 20:07:18 -0700
Subject: [PATCH 12/15] fixing abline

---
 R/bootstrap_plot.R | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/R/bootstrap_plot.R b/R/bootstrap_plot.R
index 7a8d4bc..3508143 100755
--- a/R/bootstrap_plot.R
+++ b/R/bootstrap_plot.R
@@ -76,7 +76,12 @@
       ylab("Expression in cell type (%)\n") +
       scale_color_viridis_c(direction = -1) +
       ggtitle(paste("Cell Type:", cell_type)) +
-      add_line() +
+      geom_abline(
+        intercept = 0, 
+        slope = 1, 
+        linetype = "dashed",
+        colour = ggplot2::alpha("red",.5)
+      ) +
       theme_classic()
     
     # Add labels if a column name was provided

From 6eb304d4898d9e4a55a456b49369409040fc7cce Mon Sep 17 00:00:00 2001
From: rrbutler <6644896+rbutleriii@users.noreply.github.com>
Date: Thu, 2 Oct 2025 20:35:00 -0700
Subject: [PATCH 13/15] improve labeling

---
 R/bootstrap_plot.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/bootstrap_plot.R b/R/bootstrap_plot.R
index 3508143..c8c84ad 100755
--- a/R/bootstrap_plot.R
+++ b/R/bootstrap_plot.R
@@ -62,7 +62,7 @@
   cell_types <- unique(gene_data[[facet_var]])
   
   # Start PDF device
-  pdf(output_file, width = 7, height = 7)
+  pdf(output_file, width = 5, height = 5)
   
   # Create and print a plot for each cell type
   for (cell_type in cell_types) {
@@ -149,7 +149,7 @@ bootstrap_plot <- function(gene_data,
     plots <- list()
     #### Set up save path ####
     dir.create(save_dir, showWarnings = FALSE, recursive = TRUE)  
-    gene_data$symLab <- ifelse(gene_data$hit > 25, gene_data$gene, "") 
+    gene_data$symLab <- ifelse(gene_data$hit - gene_data$boot > 1, gene_data$gene, "") 
     
     #### Filter gene_data ####
     if(!is.null(signif_ct)){

From b1a303c218dcd5326f15fc6d8ac98e35ab9e0e89 Mon Sep 17 00:00:00 2001
From: rrbutler <6644896+rbutleriii@users.noreply.github.com>
Date: Thu, 2 Oct 2025 21:06:19 -0700
Subject: [PATCH 14/15] more dots

---
 R/bootstrap_plot.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/bootstrap_plot.R b/R/bootstrap_plot.R
index c8c84ad..b513df1 100755
--- a/R/bootstrap_plot.R
+++ b/R/bootstrap_plot.R
@@ -89,6 +89,7 @@
       g <- g + ggrepel::geom_text_repel(
         aes(label = .data[[add_labels]]),  # Use the column name dynamically
         size = 3,
+        force_pull = 0.1, 
         box.padding = 0.35,
         point.padding = 0.5,
         segment.color = "grey50",

From e611462edac3f86d651c7cdaa0818511c8b658fe Mon Sep 17 00:00:00 2001
From: rrbutler <6644896+rbutleriii@users.noreply.github.com>
Date: Thu, 2 Oct 2025 22:03:35 -0700
Subject: [PATCH 15/15] include top hits labels always

---
 R/bootstrap_plot.R | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/R/bootstrap_plot.R b/R/bootstrap_plot.R
index b513df1..68d3c36 100755
--- a/R/bootstrap_plot.R
+++ b/R/bootstrap_plot.R
@@ -150,7 +150,11 @@ bootstrap_plot <- function(gene_data,
     plots <- list()
     #### Set up save path ####
     dir.create(save_dir, showWarnings = FALSE, recursive = TRUE)  
-    gene_data$symLab <- ifelse(gene_data$hit - gene_data$boot > 1, gene_data$gene, "") 
+    gene_data$symLab <- ifelse(
+      test = gene_data$hit - gene_data$boot > 1 | gene_data$hit > 75, 
+      yes = gene_data$gene, 
+      no = ""
+    ) 
     
     #### Filter gene_data ####
     if(!is.null(signif_ct)){