Update README.md

README.Rmd

@@ -72,19 +72,15 @@ Bioinformatics link: [Click here](https://academic.oup.com/bioinformatics/articl
 
 ## Installation {#installation}
 
-You can install the stable version of *ggpicrust2* from CRAN with:
+> ⚠️ **Important Notice (December 25, 2024)**: 
+> Due to some dependency package issues, `ggpicrust2` has been temporarily removed from CRAN. We are actively working to resolve these issues. However, due to CRAN's holiday break (December 23, 2024 to January 07, 2025), the resubmission will be delayed until after January 7, 2025.
+>
+> In the meantime, you can install the development version from GitHub:
 
-``` r
-install.packages("ggpicrust2")
-```
-
-To install the latest development version of *ggpicrust2* from GitHub, you can use:
+You can install the development version of *ggpicrust2* from GitHub with:
 
 ``` r
-# Install the devtools package if not already installed
 # install.packages("devtools")
-
-# Install ggpicrust2 from GitHub
 devtools::install_github("cafferychen777/ggpicrust2")
 ```
 
@@ -585,7 +581,7 @@ Use the fake dataset
 ```{r ,echo = TRUE,eval=FALSE}
 # Create example functional pathway abundance data
 abundance_example <- matrix(rnorm(30), nrow = 3, ncol = 10)
-colnames(abundance_example) <- paste0("Sample", 1:10)
+colnames(kegg_abundance_example) <- paste0("Sample", 1:10)
 rownames(kegg_abundance_example) <- c("PathwayA", "PathwayB", "PathwayC")
 
 # Create example metadata
@@ -767,8 +763,7 @@ p <- ggpicrust2::pathway_errorbar(
   ko_to_kegg = TRUE,
   p_value_bar = FALSE,
   colors = NULL,
-  x_lab = "pathway_name"
-)
+  x_lab = "pathway_name")
 ```
 
 ### Issue 7: There are no statistically significant biomarkers

README.md

@@ -109,20 +109,19 @@ here](https://academic.oup.com/bioinformatics/article/39/8/btad470/7234609?login
 
 ## Installation
 
-You can install the stable version of *ggpicrust2* from CRAN with:
+> ⚠️ **Important Notice (December 25, 2024)**: Due to some dependency
+> package issues, `ggpicrust2` has been temporarily removed from CRAN.
+> We are actively working to resolve these issues. However, due to
+> CRAN’s holiday break (December 23, 2024 to January 07, 2025), the
+> resubmission will be delayed until after January 7, 2025.
+>
+> In the meantime, you can install the development version from GitHub:
 
-``` r
-install.packages("ggpicrust2")
-```
-
-To install the latest development version of *ggpicrust2* from GitHub,
-you can use:
+You can install the development version of *ggpicrust2* from GitHub
+with:
 
 ``` r
-# Install the devtools package if not already installed
 # install.packages("devtools")
-
-# Install ggpicrust2 from GitHub
 devtools::install_github("cafferychen777/ggpicrust2")
 ```
 
@@ -669,7 +668,7 @@ Use the fake dataset
 ``` r
 # Create example functional pathway abundance data
 abundance_example <- matrix(rnorm(30), nrow = 3, ncol = 10)
-colnames(abundance_example) <- paste0("Sample", 1:10)
+colnames(kegg_abundance_example) <- paste0("Sample", 1:10)
 rownames(kegg_abundance_example) <- c("PathwayA", "PathwayB", "PathwayC")
 
 # Create example metadata
@@ -842,8 +841,7 @@ the smallest adjusted p-values:
       ko_to_kegg = TRUE,
       p_value_bar = FALSE,
       colors = NULL,
-      x_lab = "pathway_name"
-    )
+      x_lab = "pathway_name")
 
 ### Issue 7: There are no statistically significant biomarkers
 
@@ -913,7 +911,3 @@ please contact <cafferychen7850@gmail.com>.
 ![](https://raw.githubusercontent.com/cafferychen777/ggpicrust2_paper/main/paper_figure/MicrobiomeGallery_preview.jpg)
 
 We look forward to sharing more updates as these projects progress.
-
-## Star History
-
-[![Star History Chart](https://api.star-history.com/svg?repos=cafferychen777/ggpicrust2&type=Date)](https://star-history.com/#cafferychen777/ggpicrust2&Date)