From 2889f55c05022edbfd6daa4c996aa6628795c6ea Mon Sep 17 00:00:00 2001
From: huangyaqing-123 <hyaqing1023@gmail.com>
Date: Fri, 25 Jul 2025 13:39:55 -0400
Subject: [PATCH] vignette updates

---
 .Rbuildignore          |  2 ++
 .gitignore             |  3 ++
 DESCRIPTION            |  4 ++-
 vignettes/.gitignore   |  2 ++
 vignettes/examples.Rmd | 69 ++++++++++++++++++++++++++++++++++++++++++
 5 files changed, 79 insertions(+), 1 deletion(-)
 create mode 100644 vignettes/.gitignore
 create mode 100644 vignettes/examples.Rmd

diff --git a/.Rbuildignore b/.Rbuildignore
index e13c405..f2ab003 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,3 +1,5 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$
+^doc$
+^Meta$
diff --git a/.gitignore b/.gitignore
index d95edeb..09f5760 100644
--- a/.gitignore
+++ b/.gitignore
@@ -50,3 +50,6 @@ po/*~
 
 # RStudio Connect folder
 rsconnect/
+inst/doc
+/doc/
+/Meta/
diff --git a/DESCRIPTION b/DESCRIPTION
index 6bf7b4a..d65ba52 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -27,7 +27,9 @@ Imports:
     tidyverse,
     purrr
 Suggests: 
+    knitr,
+    rmarkdown,
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
 LazyData: true
-
+VignetteBuilder: knitr
diff --git a/vignettes/.gitignore b/vignettes/.gitignore
new file mode 100644
index 0000000..097b241
--- /dev/null
+++ b/vignettes/.gitignore
@@ -0,0 +1,2 @@
+*.html
+*.R
diff --git a/vignettes/examples.Rmd b/vignettes/examples.Rmd
new file mode 100644
index 0000000..c0c4541
--- /dev/null
+++ b/vignettes/examples.Rmd
@@ -0,0 +1,69 @@
+---
+title: "examples"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{examples}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+## Overview
+This vignette demonstrates how to use the PathwayEmbed package to compute and visualize pathway activation using single-cell transcriptomic data. We use the example dataset fake_test_object included with the package.
+
+## Load Package and Example Data
+```{r setup}
+library(PathwayEmbed)
+# Load the example Seurat object included in the package
+data(fake_test_object)
+```
+
+## Compute Pathway Activation
+```{r}
+# Calculate pathway activation using MDS
+# Default batch.size is set to 1000
+mds_results <- ComputeCellData(
+  fake_test_object,
+  pathway = "Wnt",
+  distance.method = "manhattan"
+)
+```
+
+## Prepare Data for Plotting
+```{r}
+# Format MDS results and metadata for plotting
+plot_data <- PreparePlotData(
+  fake_test_object,
+  mds_results,
+  group = "genotype"
+)
+```
+
+## Visualize Pathway Activation
+```{r}
+# Visualize 2D MDS embedding colored by genotype
+PlotPathway(
+  to.plot = plot_data,
+  pathway = "Wnt",
+  group = "genotype",
+  color = c("#ae282c", "#2066a8")
+)
+```
+
+## Calculate Group-wise Activation Percentage (Optional)
+```{r}
+# Calculate % of cells per group with high pathway activation
+CalculatePercentage(
+  to.plot = plot_data,
+  group_var = "genotype"
+)
+```
+
+---
+