From 17719f3c9f22751936eb7d7fd770a04534be943a Mon Sep 17 00:00:00 2001
From: delfarahalireza <delfarah@calicolabs.com>
Date: Thu, 14 Mar 2024 20:20:38 -0700
Subject: [PATCH] issue-24 fixing bug for volcano labels

---
 R/differential_expression.R | 41 +++++++++++++++++++++----------------
 1 file changed, 23 insertions(+), 18 deletions(-)

diff --git a/R/differential_expression.R b/R/differential_expression.R
index 97ae99f..7db0ceb 100644
--- a/R/differential_expression.R
+++ b/R/differential_expression.R
@@ -292,11 +292,10 @@ diffex_fdr <- function(term_data) {
 #' 
 #' @export
 plot_volcano <- function(
-  regression_significance,
-  max_p_trans = 10,
-  FDR_cutoff = 0.1,
-  feature_labels = NULL
-  ) {
+    regression_significance,
+    max_p_trans = 10,
+    FDR_cutoff = 0.1,
+    feature_labels = NULL) {
   
   checkmate::assertDataFrame(regression_significance)
   stopifnot("term" %in% colnames(regression_significance))
@@ -311,24 +310,30 @@ plot_volcano <- function(
     stop("volcano plot cannot be generated due to unknown test")
   }
   
-  regression_significance %>%
-    dplyr::filter(!is.na(p.value)) %>%
-    dplyr::mutate(
-      p.value.trans = trans_pvalues(p.value, max_p_trans = max_p_trans),
-      is_discovery = qvalue < FDR_cutoff
-    ) %>%
-    ggplot(aes_string(x = effect_var)) +
-    {if ("compoundName" %in% colnames(regression_significance)) {
-      geom_point(aes(y = p.value.trans, color = is_discovery, name = compoundName)) +
-        geom_text(aes(label = ifelse(compoundName %in% feature_labels, compoundName, ""), y = p.value.trans, vjust = -0.75))
-      } 
-      else {geom_point(aes(y = p.value.trans, color = is_discovery))}
-      } +
+  grob <- ggplot(
+    regression_significance %>%
+      dplyr::filter(!is.na(p.value)) %>%
+      dplyr::mutate(
+        p.value.trans = trans_pvalues(p.value, max_p_trans = max_p_trans),
+        is_discovery = qvalue < FDR_cutoff
+      ),
+    aes_string(x = effect_var)
+  ) +
     facet_wrap(~term, scales = "free_x") +
     scale_x_continuous("Effect size") +
     scale_y_continuous(expression(-log[10] ~ "pvalue")) +
     scale_color_manual(values = c("FALSE" = "gray50", "TRUE" = "RED")) +
     theme_bw()
+  
+  if ("compoundName" %in% colnames(regression_significance)) {
+    grob <- grob +
+      geom_point(aes(y = p.value.trans, color = is_discovery, name = compoundName)) +
+      geom_text(aes(label = ifelse(compoundName %in% feature_labels, compoundName, ""), y = p.value.trans, vjust = -0.75))
+  } else {
+    grob <- grob + 
+      geom_point(aes(y = p.value.trans, color = is_discovery))
+  }
+  return(grob)
 }
 
 trans_pvalues <- function(p, max_p_trans = 10) {