From c2617acf7c6118c5d17bbc43e47cdf8e977127a4 Mon Sep 17 00:00:00 2001
From: nbpeterson3 <68209187+nbpeterson3@users.noreply.github.com>
Date: Thu, 18 Jul 2024 14:05:36 -0500
Subject: [PATCH 1/4] Update do_VolcanoPlot.R

Replaced object reference to 'genes' with 'de_genes'
---
 R/do_VolcanoPlot.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/do_VolcanoPlot.R b/R/do_VolcanoPlot.R
index 91caf11..3520152 100644
--- a/R/do_VolcanoPlot.R
+++ b/R/do_VolcanoPlot.R
@@ -173,7 +173,7 @@ do_VolcanoPlot <- function(sample,
 
   if (isTRUE(add_gene_tags)){
     if (order_tags_by == "both"){
-      data.label <- genes %>%
+      data.label <- de_genes %>%
                     dplyr::mutate("abs_avg_log2FC" = abs(.data$avg_log2FC)) %>% 
                     dplyr::arrange(dplyr::desc(.data$log_p),
                                    dplyr::desc(.data$abs_avg_log2FC)) %>%

From 151033d9d43067b0ef032c45cf3ccd71d511e1cb Mon Sep 17 00:00:00 2001
From: nbpeterson3 <68209187+nbpeterson3@users.noreply.github.com>
Date: Thu, 18 Jul 2024 14:14:30 -0500
Subject: [PATCH 2/4] Update do_VolcanoPlot.R

Replaced reference to 'de_genes' with 'data'
---
 R/do_VolcanoPlot.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/do_VolcanoPlot.R b/R/do_VolcanoPlot.R
index 3520152..0360d7d 100644
--- a/R/do_VolcanoPlot.R
+++ b/R/do_VolcanoPlot.R
@@ -173,7 +173,7 @@ do_VolcanoPlot <- function(sample,
 
   if (isTRUE(add_gene_tags)){
     if (order_tags_by == "both"){
-      data.label <- de_genes %>%
+      data.label <- data %>%
                     dplyr::mutate("abs_avg_log2FC" = abs(.data$avg_log2FC)) %>% 
                     dplyr::arrange(dplyr::desc(.data$log_p),
                                    dplyr::desc(.data$abs_avg_log2FC)) %>%

From 34ce6dc1d663928e65d0ca43ac9ac94e91f60040 Mon Sep 17 00:00:00 2001
From: nbpeterson3 <68209187+nbpeterson3@users.noreply.github.com>
Date: Thu, 18 Jul 2024 14:32:51 -0500
Subject: [PATCH 3/4] Update do_VolcanoPlot.R

Replaced reference to 'number.tags' with 'n_genes'...
---
 R/do_VolcanoPlot.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/do_VolcanoPlot.R b/R/do_VolcanoPlot.R
index 0360d7d..86806ec 100644
--- a/R/do_VolcanoPlot.R
+++ b/R/do_VolcanoPlot.R
@@ -178,7 +178,7 @@ do_VolcanoPlot <- function(sample,
                     dplyr::arrange(dplyr::desc(.data$log_p),
                                    dplyr::desc(.data$abs_avg_log2FC)) %>%
                     as.data.frame() %>%
-                    utils::head(number.tags * 2)
+                    utils::head(n_genes * 2)
     } else if (order_tags_by == "pvalue"){
       data.up <- data %>%
                  dplyr::filter(.data$avg_log2FC > 0) %>%

From 7234410286e73619a34c89dddbc11800c8e37127 Mon Sep 17 00:00:00 2001
From: nbpeterson3 <68209187+nbpeterson3@users.noreply.github.com>
Date: Thu, 18 Jul 2024 14:52:54 -0500
Subject: [PATCH 4/4] Update do_VolcanoPlot.R

Added rbind call to create 'data.label' for the conditions where 'order_tags_by' == "pvalue" or "logfc"
---
 R/do_VolcanoPlot.R | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/R/do_VolcanoPlot.R b/R/do_VolcanoPlot.R
index 86806ec..94362f2 100644
--- a/R/do_VolcanoPlot.R
+++ b/R/do_VolcanoPlot.R
@@ -192,6 +192,8 @@ do_VolcanoPlot <- function(sample,
                    dplyr::arrange(dplyr::desc(.data$log_p)) %>%
                    as.data.frame() %>%
                    utils::head(n_genes)
+      
+      data.label <- dplyr::bind_rows(data.up, data.down)
     } else if (order_tags_by == "logfc"){
       data.up <- data %>%
                  dplyr::arrange(dplyr::desc(.data$avg_log2FC)) %>%
@@ -202,6 +204,8 @@ do_VolcanoPlot <- function(sample,
                    dplyr::arrange(.data$avg_log2FC) %>%
                    as.data.frame() %>%
                    utils::head(n_genes)
+
+      data.label <- dplyr::bind_rows(data.up, data.down)
     }
 
     if (add_tag_side == "positive") {