From 71039a982f6caf17871b023a46dfe770734131e9 Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Tue, 6 Jan 2026 19:22:31 -0500
Subject: [PATCH 1/4] feat(dataProcessPlots): Add confidence interval bars to
 profile plots

---
 R/dataProcessPlots.R        | 5 ++++-
 R/utils_dataprocess_plots.R | 8 ++++++++
 2 files changed, 12 insertions(+), 1 deletion(-)

diff --git a/R/dataProcessPlots.R b/R/dataProcessPlots.R
index a0ab4e13..5e8fa9a9 100644
--- a/R/dataProcessPlots.R
+++ b/R/dataProcessPlots.R
@@ -385,7 +385,10 @@ dataProcessPlots = function(
         list(PROTEIN = unique(Protein), PEPTIDE = "Run summary",
              TRANSITION = "Run summary", FEATURE = "Run summary",
              LABEL = "Endogenous", RUN = RUN,
-             ABUNDANCE = LogIntensities, FRACTION = 1)
+             ABUNDANCE = LogIntensities, FRACTION = 1, 
+             UPPERBOUND = if("Variance" %in% names(.SD)) LogIntensities + 1.96 * sqrt(Variance) else NA_real_,
+             LOWERBOUND = if("Variance" %in% names(.SD)) LogIntensities - 1.96 * sqrt(Variance) else NA_real_
+             )
         ]
       if (is_censored) {
         quant$censored = FALSE
diff --git a/R/utils_dataprocess_plots.R b/R/utils_dataprocess_plots.R
index d2ecd72d..d5304bd1 100644
--- a/R/utils_dataprocess_plots.R
+++ b/R/utils_dataprocess_plots.R
@@ -172,6 +172,14 @@
                        aes(x = .data$RUN, y = .data$newABUNDANCE, 
                                   color = .data$analysis, size = .data$analysis, 
                                   shape = .data$censored)) +
+            geom_errorbar(data = input[input$PEPTIDE == "Run summary"],
+                          aes(x = .data$RUN, 
+                              ymin = .data$LOWERBOUND, 
+                              ymax = .data$UPPERBOUND,
+                              color = .data$analysis),
+                          width = 0.3, # Probably needs to be adjustable for user
+                          linewidth = 0.5,
+                          linetype = "solid") + 
             scale_shape_manual(values = c(16, 1), 
                                labels = c("Detected data",
                                           "Censored missing data"))

From caf4f87950eecf173fd49b2754c2f554601410c3 Mon Sep 17 00:00:00 2001
From: tonywu1999 <wu.anthon@northeastern.edu>
Date: Wed, 7 Jan 2026 12:09:54 -0500
Subject: [PATCH 2/4] Adjust plot width parameter in utils_dataprocess_plots

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

diff --git a/R/utils_dataprocess_plots.R b/R/utils_dataprocess_plots.R
index d5304bd1..b0fccb2d 100644
--- a/R/utils_dataprocess_plots.R
+++ b/R/utils_dataprocess_plots.R
@@ -177,7 +177,7 @@
                               ymin = .data$LOWERBOUND, 
                               ymax = .data$UPPERBOUND,
                               color = .data$analysis),
-                          width = 0.3, # Probably needs to be adjustable for user
+                          width = 0.3,
                           linewidth = 0.5,
                           linetype = "solid") + 
             scale_shape_manual(values = c(16, 1), 
@@ -296,4 +296,4 @@
         theme_msstats("CONDITIONPLOT", x.axis.size, y.axis.size, 
                       text_angle = text.angle)
     plot
-}
\ No newline at end of file
+}

From 52670fd70f97bc22cd40977fde6bd564e9038b35 Mon Sep 17 00:00:00 2001
From: tonywu1999 <wu.anthon@northeastern.edu>
Date: Wed, 7 Jan 2026 12:11:52 -0500
Subject: [PATCH 3/4] Refactor UPPERBOUND calculation in dataProcessPlots.R

Updated UPPERBOUND calculation to include a comment for clarity.
---
 R/dataProcessPlots.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/dataProcessPlots.R b/R/dataProcessPlots.R
index 5e8fa9a9..dd3e1f66 100644
--- a/R/dataProcessPlots.R
+++ b/R/dataProcessPlots.R
@@ -386,10 +386,10 @@ dataProcessPlots = function(
              TRANSITION = "Run summary", FEATURE = "Run summary",
              LABEL = "Endogenous", RUN = RUN,
              ABUNDANCE = LogIntensities, FRACTION = 1, 
-             UPPERBOUND = if("Variance" %in% names(.SD)) LogIntensities + 1.96 * sqrt(Variance) else NA_real_,
+             UPPERBOUND = if("Variance" %in% names(.SD)) LogIntensities + 1.96 * sqrt(Variance) else NA_real_, # 95% confidence interval
              LOWERBOUND = if("Variance" %in% names(.SD)) LogIntensities - 1.96 * sqrt(Variance) else NA_real_
-             )
-        ]
+        )
+      ]
       if (is_censored) {
         quant$censored = FALSE
       }

From b5e943c9b4a90fb9ab29d4ec617f67750beb02cd Mon Sep 17 00:00:00 2001
From: tonywu1999 <wu.anthon@northeastern.edu>
Date: Wed, 7 Jan 2026 12:39:50 -0500
Subject: [PATCH 4/4] add vignette of profile plot

---
 vignettes/MSstatsPlus.Rmd | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/vignettes/MSstatsPlus.Rmd b/vignettes/MSstatsPlus.Rmd
index 198c79bf..3a2a052a 100644
--- a/vignettes/MSstatsPlus.Rmd
+++ b/vignettes/MSstatsPlus.Rmd
@@ -297,6 +297,12 @@ will be included called `Variance` indicating the variance of the underlying
 protein abundance estimate. This variance is used in the next step of the
 workflow.
 
+Meanwhile, one can generate a profile plot to visualize the variance of the underlying protein abundance estimates in the form of 95% confidence intervals. For example, with Q9UFW8, one may observe that confidence intervals are wider for runs with more imputed values.
+
+```{r}
+dataProcessPlots(summarized, "ProfilePlot", which.Protein = "Q9UFW8", address = FALSE)
+```
+
 ## Differential analysis
 
 The final step of the `MSstats+` workflow is to perform differential analysis.