From 693f9d064f7a77120f4fd61a6420acda77c0eaca Mon Sep 17 00:00:00 2001
From: xuewei cao <36172337+xueweic@users.noreply.github.com>
Date: Thu, 17 Apr 2025 04:11:11 -0400
Subject: [PATCH] minor update

---
 R/colocboost_plot.R                           |  2 +-
 _pkgdown.yml                                  |  1 +
 .../Disease_Prioritized_Colocalization.Rmd    | 16 ++++++++++
 vignettes/Individual_Level_Colocalization.Rmd |  3 ++
 vignettes/Input_Data_Format.Rmd               | 10 ++++++
 vignettes/Interpret_ColocBoost_Output.Rmd     |  2 ++
 vignettes/Partial_Overlap_Variants.Rmd        | 31 +++++++++++++++++++
 .../Summary_Statistics_Colocalization.Rmd     |  3 ++
 vignettes/announcements.Rmd                   |  1 +
 9 files changed, 68 insertions(+), 1 deletion(-)
 create mode 100644 vignettes/Partial_Overlap_Variants.Rmd

diff --git a/R/colocboost_plot.R b/R/colocboost_plot.R
index fd893c6..3b3db70 100644
--- a/R/colocboost_plot.R
+++ b/R/colocboost_plot.R
@@ -531,7 +531,7 @@ plot_initial <- function(cb_plot_input, y = "log10p",
     plot_data <- cb_plot_input$vcp
     ylab <- "VCP"
     if (length(cb_plot_input$outcomes) == 1) {
-      ylab <- "PIP"
+      ylab <- "VPA"
     }
     args$ylim <- c(0, 1)
   } else if (y == "coef") {
diff --git a/_pkgdown.yml b/_pkgdown.yml
index eccb370..56f6e39 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -26,6 +26,7 @@ articles:
     - Disease_Prioritized_Colocalization
     - Interpret_ColocBoost_Output
     - Visualization_ColocBoost_Output
+    - Partial_Overlap_Variants
 
   - title: internal
     contents:
diff --git a/vignettes/Disease_Prioritized_Colocalization.Rmd b/vignettes/Disease_Prioritized_Colocalization.Rmd
index ed4469f..fb5da2f 100644
--- a/vignettes/Disease_Prioritized_Colocalization.Rmd
+++ b/vignettes/Disease_Prioritized_Colocalization.Rmd
@@ -78,6 +78,9 @@ res <- colocboost(X = X, Y = Y, sumstat = sumstat, LD = LD)
 
 # Identified CoS
 res$cos_details$cos$cos_index
+
+# Plotting the results
+colocboost_plot(res)
 ```
 
 ### Results Interpretation
@@ -89,10 +92,23 @@ For comprehensive tutorials on result interpretation and advanced visualization
 # 3. Run ColocBoost (Disease Prioritized Colocalization)
 
 
+TO-DO-LIST
+
+
 ```{r disease-basic}
 # Run colocboost
 res <- colocboost(X = X, Y = Y, sumstat = sumstat, LD = LD, focal_outcome_idx = 5)
 
 # Identified CoS
 res$cos_details$cos$cos_index
+
+# Plotting results
+colocboost_plot(res)
+```
+
+
+
+```{r disease-basic-focal}
+# Plotting the focal only results
+colocboost_plot(res, plot_focal_only = TRUE)
 ```
\ No newline at end of file
diff --git a/vignettes/Individual_Level_Colocalization.Rmd b/vignettes/Individual_Level_Colocalization.Rmd
index cb2d430..8e484ba 100644
--- a/vignettes/Individual_Level_Colocalization.Rmd
+++ b/vignettes/Individual_Level_Colocalization.Rmd
@@ -75,6 +75,9 @@ res <- colocboost(X = X, Y = Y)
 
 # Identified CoS
 res$cos_details$cos$cos_index
+
+# Plotting the results
+colocboost_plot(res)
 ```
 
 
diff --git a/vignettes/Input_Data_Format.Rmd b/vignettes/Input_Data_Format.Rmd
index a472cac..b849350 100644
--- a/vignettes/Input_Data_Format.Rmd
+++ b/vignettes/Input_Data_Format.Rmd
@@ -66,3 +66,13 @@ refer to [Summary Statistics Colocalization](https://statfungen.github.io/colocb
 - One LD matrix with a superset of variants in `sumstat` for all traits is allowed.
 - Multiple LD matrices, each corresponding to a different trait, are also allowed for the trait-specific LD structure.
 - Multiple LD matrices and unmatched `sumstat` data frames with a mapping dictionary are also allowed.  
+
+
+
+## 3. Dictionary format for mapping
+
+TO-DO-LIST
+
+## 4. Effect size and standard error of effect size matrices
+
+TO-DO-LIST
diff --git a/vignettes/Interpret_ColocBoost_Output.Rmd b/vignettes/Interpret_ColocBoost_Output.Rmd
index ff48277..8e8ccfb 100644
--- a/vignettes/Interpret_ColocBoost_Output.Rmd
+++ b/vignettes/Interpret_ColocBoost_Output.Rmd
@@ -88,6 +88,8 @@ The output from `get_strong_colocalization` is the same as output from `colocboo
 
 ## 3. Details of ColocBoost output
 
+TO-DO-LIST
+
 The entire colocalization output from `colocboost` is stored in the `colocboost` object, which contains several components:
 
 - `cos_summary`: A summary table for colocalization events.
diff --git a/vignettes/Partial_Overlap_Variants.Rmd b/vignettes/Partial_Overlap_Variants.Rmd
new file mode 100644
index 0000000..da30c9c
--- /dev/null
+++ b/vignettes/Partial_Overlap_Variants.Rmd
@@ -0,0 +1,31 @@
+---
+title: "Handling partial overlapping variants across traits in ColocBoost"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Handling partial overlapping variants across traits in ColocBoost}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+This vignette demonstrates how to handle partial overlapping variants across traits in ColocBoost.
+
+
+```{r setup}
+library(colocboost)
+```
+
+![](../man/figures/missing_representation.png)
+
+
+TO-DO-LIST
+
+
+
+
diff --git a/vignettes/Summary_Statistics_Colocalization.Rmd b/vignettes/Summary_Statistics_Colocalization.Rmd
index 396535a..1029e73 100644
--- a/vignettes/Summary_Statistics_Colocalization.Rmd
+++ b/vignettes/Summary_Statistics_Colocalization.Rmd
@@ -81,6 +81,9 @@ res <- colocboost(sumstat = Sumstat_5traits$sumstat, LD = LD)
 
 # Identified CoS
 res$cos_details$cos$cos_index
+
+# Plotting the results
+colocboost_plot(res)
 ```
 
 
diff --git a/vignettes/announcements.Rmd b/vignettes/announcements.Rmd
index 50ebd7b..e3f2bfb 100644
--- a/vignettes/announcements.Rmd
+++ b/vignettes/announcements.Rmd
@@ -10,6 +10,7 @@ vignette: >
 
 ## Initial release in ColocBoost
 
+TO-DO-LIST
 
 We are excited to release ColocBoost (FIXME version), where it is now the default version for new installs.