diff --git a/R/CalculatePercentage.R b/R/CalculatePercentage.R
index 448e5b3..b233435 100644
--- a/R/CalculatePercentage.R
+++ b/R/CalculatePercentage.R
@@ -1,14 +1,16 @@
-#' Calculate the percentage of cells in activation status
+#' CalculatePercentage
 #'
 #' This function calculates the percentage of cells in ON (scale > 0) and OFF (scale < 0)
 #' activation states within each group defined by `group_var`. If exactly two groups
 #' are provided, it also computes Cohen's d effect size between their activation values.
+#'
 #' @name CalculatePercentage
 #' @importFrom dplyr bind_rows
 #' @importFrom effsize cohen.d
 #' @importFrom stats na.omit
 #' @param to.plot A data frame containing at least a `scale` column and a grouping column.
 #' @param group_var A string specifying the grouping variable (e.g., "genotype", "treatment").
+#'
 #' @return A data frame with the percentage of ON/OFF cells and Cohen's d (if applicable).
 #' @examples
 #' data(fake_to_plot)
diff --git a/R/ComputeCellData.R b/R/ComputeCellData.R
index 584def6..94565ac 100644
--- a/R/ComputeCellData.R
+++ b/R/ComputeCellData.R
@@ -1,3 +1,5 @@
+#' ComputeCellData
+#'
 #' A function computes cell status for a given pathway in single-cell RNA-seq data,
 #' based on the distance between genes in a specified pathway. The distance is computed
 #' for each batch of cells, and classical multidimensional scaling (MDS) is used to
@@ -14,7 +16,7 @@
 #'
 #' @param x A `Seurat` object containing single-cell RNA sequencing data.
 #' @param pathway A `character` string specifying the pathway name. This should match a pathway used by `LoadPathway()`.
-#' @param distance.method A `character` string specifying the distance metric to use.
+#' @param distance.method A `character` string specifying the distance metric to use.Default is "manhattan".
 #' Options include: `"manhattan"`, `"euclidean"`, `"canberra"`, `"binary"`, `"minkowski"`
 #' @param batch.size An `integer` specifying the number of cells to process per batch. Default is 1000.
 #' @param scale.data A `logical` indicating whether to use scaled data (`scale.data = TRUE`) or normalized data. Default is `TRUE`.
@@ -53,8 +55,15 @@ ComputeCellData <- function(x, pathway, distance.method, batch.size = batch.size
   shuffled_cell_id <- sample(cell_id)
 
   # Split shuffled indices into batches
+  # Check if batch.size is provided; if not, set default and message
+  if (missing(batch.size) || is.null(batch.size)) {
+    message("Parameter 'batch.size' is missing or NULL. Setting default batch size to 1000.")
+    batch.size <- 1000
+  }
+
   # Define batch size
   batch_size <- batch.size
+
   batches <- split(shuffled_cell_id, ceiling(seq_along(shuffled_cell_id) / batch.size))
 
   # Subset expression data into chunks based on sampled indices
@@ -82,6 +91,12 @@ ComputeCellData <- function(x, pathway, distance.method, batch.size = batch.size
       next
     }
 
+    # Check if distance.method is provided; if not, set default and message
+    if (missing(distance.method) || is.null(distance.method)) {
+      message("Parameter 'distance.method' is missing or NULL. Setting default distance.method to 'manhattan'.")
+      distance.method <- "manhattan"
+    }
+
     # Distance calculation
     message("Computing distance...")
     d <- dist(t(pathwaytempdata), method = distance.method)
diff --git a/R/LoadPathway.R b/R/LoadPathway.R
index 7595976..79f51d8 100644
--- a/R/LoadPathway.R
+++ b/R/LoadPathway.R
@@ -1,6 +1,7 @@
-## Pathway Data Extraction from Exceldataset
+#' LoadPathway
 #'
 #' This function reads pathway data from the package's built-in Excel file.
+#'
 #' @name LoadPathway
 #' @param pathway A `character` string specifying the pathway name.
 #' @return A data frame with pathway data.
diff --git a/R/PathwayMaxMin.R b/R/PathwayMaxMin.R
index 80e93dc..71a8bdc 100644
--- a/R/PathwayMaxMin.R
+++ b/R/PathwayMaxMin.R
@@ -1,4 +1,7 @@
+#' PathwayMaxMin
+#'
 #' A function to obtain the hypothetical max and min activation status of selected pathway for a given scRNA seq data set
+#'
 #' @name PathwayMaxMin
 #' @import Seurat
 #' @import tidyverse
diff --git a/R/PlotPathway.R b/R/PlotPathway.R
index c2ac45d..d72d7f1 100644
--- a/R/PlotPathway.R
+++ b/R/PlotPathway.R
@@ -1,3 +1,5 @@
+#' PlotPathway
+#'
 #' A function to plot the Pathway activation status
 #'
 #' @name PlotPathway
diff --git a/README.md b/README.md
index a53803b..a58b1d4 100644
--- a/README.md
+++ b/README.md
@@ -37,7 +37,7 @@ library(PathwayEmbed)
 data(fake_test_object)
 
 # Compute pathway data
-mds_results <- ComputeCellData(fake_test_object, pathway = "Wnt", distance.method = "manhattan")
+mds_results <- ComputeCellData(fake_test_object, pathway = "Wnt", distance.method = "manhattan", batch.size = 100) need to add a default batch size and a end message
 
 # Prepare data for plotting
 plot_data <- PreparePlotData(fake_test_object, mds_results, group = "genotype")
diff --git a/inst/extdata/Pathway_Embedding.xlsx b/inst/extdata/Pathway_Embedding.xlsx
index b2c8852..4ad26c8 100644
Binary files a/inst/extdata/Pathway_Embedding.xlsx and b/inst/extdata/Pathway_Embedding.xlsx differ
diff --git a/man/CalculatePercentage.Rd b/man/CalculatePercentage.Rd
index e8ee495..d0df29c 100644
--- a/man/CalculatePercentage.Rd
+++ b/man/CalculatePercentage.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/CalculatePercentage.R
 \name{CalculatePercentage}
 \alias{CalculatePercentage}
-\title{Calculate the percentage of cells in activation status}
+\title{CalculatePercentage}
 \usage{
 CalculatePercentage(to.plot, group_var)
 }
diff --git a/man/ComputeCellData.Rd b/man/ComputeCellData.Rd
index 2890bc1..c5e25d6 100644
--- a/man/ComputeCellData.Rd
+++ b/man/ComputeCellData.Rd
@@ -2,10 +2,7 @@
 % Please edit documentation in R/ComputeCellData.R
 \name{ComputeCellData}
 \alias{ComputeCellData}
-\title{A function computes cell status for a given pathway in single-cell RNA-seq data,
-based on the distance between genes in a specified pathway. The distance is computed
-for each batch of cells, and classical multidimensional scaling (MDS) is used to
-visualize the pathway expression across cells.}
+\title{ComputeCellData}
 \usage{
 ComputeCellData(
   x,
@@ -20,7 +17,7 @@ ComputeCellData(
 
 \item{pathway}{A \code{character} string specifying the pathway name. This should match a pathway used by \code{LoadPathway()}.}
 
-\item{distance.method}{A \code{character} string specifying the distance metric to use.
+\item{distance.method}{A \code{character} string specifying the distance metric to use.Default is "manhattan".
 Options include: \code{"manhattan"}, \code{"euclidean"}, \code{"canberra"}, \code{"binary"}, \code{"minkowski"}}
 
 \item{batch.size}{An \code{integer} specifying the number of cells to process per batch. Default is 1000.}
diff --git a/man/LoadPathway.Rd b/man/LoadPathway.Rd
index e10575b..53554a1 100644
--- a/man/LoadPathway.Rd
+++ b/man/LoadPathway.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/LoadPathway.R
 \name{LoadPathway}
 \alias{LoadPathway}
-\title{This function reads pathway data from the package's built-in Excel file.}
+\title{LoadPathway}
 \usage{
 LoadPathway(pathway)
 }
diff --git a/man/PathwayMaxMin.Rd b/man/PathwayMaxMin.Rd
index cee43c3..d473aa9 100644
--- a/man/PathwayMaxMin.Rd
+++ b/man/PathwayMaxMin.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/PathwayMaxMin.R
 \name{PathwayMaxMin}
 \alias{PathwayMaxMin}
-\title{A function to obtain the hypothetical max and min activation status of selected pathway for a given scRNA seq data set}
+\title{PathwayMaxMin}
 \usage{
 PathwayMaxMin(x, pathway, scale.data = TRUE)
 }
diff --git a/man/PlotPathway.Rd b/man/PlotPathway.Rd
index 3e18af8..4f7ed94 100644
--- a/man/PlotPathway.Rd
+++ b/man/PlotPathway.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/PlotPathway.R
 \name{PlotPathway}
 \alias{PlotPathway}
-\title{A function to plot the Pathway activation status}
+\title{PlotPathway}
 \usage{
 PlotPathway(to.plot, pathway, group, color)
 }