From e4d30aea1c65b09e4ce4adcf56d59d1d90f39189 Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Thu, 23 Apr 2026 19:37:46 -0400
Subject: [PATCH] fix(comparisonPlot): Add 95% CI description in tooltip

---
 R/groupComparisonPlots.R        | 4 ++--
 R/utils_groupcomparison_plots.R | 8 ++++----
 man/dot-makeComparison.Rd       | 5 ++++-
 3 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/R/groupComparisonPlots.R b/R/groupComparisonPlots.R
index 087b8206..8dec5e40 100644
--- a/R/groupComparisonPlots.R
+++ b/R/groupComparisonPlots.R
@@ -421,8 +421,8 @@ groupComparisonPlots = function(
         vjust = ifelse(text.angle != 0, 1, 0.5)
         
         plot = .makeComparison(single_protein, log_base_FC, dot.size, x.axis.size,
-                               y.axis.size, text.angle, hjust, vjust, y.limdown, 
-                               y.limup)
+                               y.axis.size, text.angle, hjust, vjust, y.limdown,
+                               y.limup, sig)
         print(plot)
         plots[[i]] = plot
     }
diff --git a/R/utils_groupcomparison_plots.R b/R/utils_groupcomparison_plots.R
index ffb340c4..e5687fed 100644
--- a/R/utils_groupcomparison_plots.R
+++ b/R/utils_groupcomparison_plots.R
@@ -282,18 +282,18 @@ colMin <- function(data) sapply(data, min, na.rm = TRUE)
 #' @inheritParams groupComparisonPlots
 #' @keywords internal
 .makeComparison = function(
-    input, log_base, dot.size, x.axis.size, y.axis.size, 
-    text.angle, hjust, vjust, y.limdown, y.limup
+    input, log_base, dot.size, x.axis.size, y.axis.size,
+    text.angle, hjust, vjust, y.limdown, y.limup, sig
 ) {
     logFC = ciw = NULL
-    
+    ci_label = paste0("(", (1 - sig) * 100, "% CI)")
     protein = unique(input$Protein)
     plot = ggplot(input, aes(x = .data$Label, y = .data$logFC)) +
         geom_errorbar(aes(ymax = .data$logFC + .data$ciw, ymin = .data$logFC - .data$ciw),
                       data = input,
                       width = 0.1,
                       colour = "red") +
-        geom_point(aes(text = paste0("logFC: ", round(.data$logFC, 4), " ± ", round(.data$ciw, 4))),
+        geom_point(aes(text = paste0("logFC: ", round(.data$logFC, 4), " ± ", round(.data$ciw, 4), " ", ci_label)),
                    size = dot.size,
                    colour = "darkred") +
         scale_x_discrete('Comparison') +
diff --git a/man/dot-makeComparison.Rd b/man/dot-makeComparison.Rd
index 714e4343..917a73aa 100644
--- a/man/dot-makeComparison.Rd
+++ b/man/dot-makeComparison.Rd
@@ -14,7 +14,8 @@
   hjust,
   vjust,
   y.limdown,
-  y.limup
+  y.limup,
+  sig
 )
 }
 \arguments{
@@ -29,6 +30,8 @@
 \item{y.axis.size}{size of axes labels, e.g. name of targeted proteins in heatmap. Default is 10.}
 
 \item{text.angle}{angle of x-axis labels represented each comparison at the bottom of graph in comparison plot. Default is 0.}
+
+\item{sig}{FDR cutoff for the adjusted p-values in heatmap and volcano plot. level of significance for comparison plot. 100(1-sig)\% confidence interval will be drawn.  sig=0.05 is default.}
 }
 \description{
 Create comparison plot