Updated installation instructions, messages for installing optional d…

…ependencies, and vignette documentation
csbg · Jan 13, 2025 · 7cccfdf · 7cccfdf
1 parent 1b29ae7
commit 7cccfdf
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Showing 12 changed files with 341 additions and 161 deletions.
diff --git a/R/open_tutorial_and_template.R b/R/open_tutorial_and_template.R
@@ -17,8 +17,14 @@ open_tutorial <- function() {
   # Check if rstudioapi is installed
   if (!requireNamespace("rstudioapi", quietly = TRUE)) {
     stop_call_false(
-      "The 'rstudioapi' package is not installed. ",
-      "Please install it manually with: install.packages('rstudioapi')."
+      "The 'rstudioapi' package is not installed.\n",
+      "Please install it manually (to your custom_lib_path) using the command", 
+      "below and re-run the function:\n\n",
+      "  install.packages('rstudioapi')\n\n",
+      "This is an optional dependency of the SplineOmics package, ",
+      "only needed for optional functionality and not part of the core", 
+      "package, which is why it must be installed manually if this function", 
+      "is used."
     )
   }
 
@@ -56,10 +62,15 @@ open_tutorial <- function() {
 open_template <- function() {
   # Check if rstudioapi is installed
   if (!requireNamespace("rstudioapi", quietly = TRUE)) {
-    stop(
-      "The 'rstudioapi' package is not installed. ",
-      "Please install it manually with: install.packages('rstudioapi').",
-      call. = FALSE
+    stop_call_false(
+      "The 'rstudioapi' package is not installed.\n",
+      "Please install it manually (to your custom_lib_path) using the", 
+      "command below and re-run the function:\n\n",
+      "  install.packages('rstudioapi')\n\n",
+      "This is an optional dependency of the SplineOmics package, ",
+      "only needed for optional functionality and not part of the", 
+      "core package, ",
+      "which is why it must be installed manually if this function is used."
     )
   }
 

diff --git a/R/preprocess_rna_seq_data.R b/R/preprocess_rna_seq_data.R
@@ -46,11 +46,15 @@ preprocess_rna_seq_data <- function(
 
   # Check if edgeR is installed; if not, inform the user
   if (!requireNamespace("edgeR", quietly = TRUE)) {
-    stop(
-      "The 'edgeR' package is not installed. ",
-      "Please install it manually using BiocManager::install('edgeR') ",
-      "and re-run the function."
+    stop_call_false(
+      "The 'edgeR' package is not installed.\n",
+      "Please install it manually (to your custom_lib_path) using the command", 
+      " below and re-run the function:\n\n",
+      "  BiocManager::install('edgeR')\n\n",
+      "This is an optional dependency of the SplineOmics package, ",
+      "only needed when working with RNA-seq data."
     )
+
   }
 
   design_matrix <- design2design_matrix(

diff --git a/R/run_gsea.R b/R/run_gsea.R
@@ -178,7 +178,7 @@ control_inputs_create_gsea_report <- function(
 
   if (!is.null(background)) {
     if (!is.character(background)) {
-      stop("background must be a character vector or NULL.", call. = FALSE)
+      stop_call_false("background must be a character vector or NULL.")
     } else {
       check_genes(background)
     }
@@ -199,11 +199,15 @@ control_inputs_create_gsea_report <- function(
 ensure_clusterProfiler <- function() {
   # Check if clusterProfiler is installed; if not, inform the user
   if (!requireNamespace("clusterProfiler", quietly = TRUE)) {
-    stop(
-      "The 'clusterProfiler' package is not installed. ",
-      "Please install it manually using", 
-      "BiocManager::install('clusterProfiler') ",
-      "and re-run the function."
+    stop_call_false(
+      "The 'clusterProfiler' package is not installed.\n",
+      "Please install it manually (to your custom_lib_path) using the", 
+      "command below and re-run the function:\n\n",
+      "  BiocManager::install('clusterProfiler')\n\n",
+      "This is an optional dependency of the SplineOmics package, ",
+      "only needed for optional functionality and not part of the core", 
+      "package, ",
+      "which is why it must be installed manually if this function is used."
     )
   }
 }

diff --git a/README.Rmd b/README.Rmd
@@ -98,8 +98,7 @@ Follow the steps below to install the `SplineOmics` package from the GitHub repo
 Note that some installation paths potentially are not writable on **Windows**. Therefore, it can be necessary to set up a library path and use that path for the installations:
 
 ``` r
-# Define the custom library path and expand the tilde (~)
-custom_lib_path <- path.expand("~/Rlibs")
+custom_lib_path <- "C:/Rlibs"  # Replace with your desired path
 
 # Create the directory if it doesn't exist
 if (!dir.exists(custom_lib_path)) {

diff --git a/README.md b/README.md
diff --git a/docs/articles/RNA-seq analysis.html b/docs/articles/RNA-seq analysis.html
diff --git a/docs/articles/get-started.html b/docs/articles/get-started.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -7,7 +7,7 @@ articles:
   Docker-instructions: Docker-instructions.html
   get-started: get-started.html
   RNA-seq analysis: RNA-seq analysis.html
-last_built: 2025-01-13T13:44Z
+last_built: 2025-01-13T15:25Z
 urls:
   reference: https://csbg.github.io/SplineOmics/reference
   article: https://csbg.github.io/SplineOmics/articles
diff --git a/docs/search.json b/docs/search.json
diff --git a/vignettes/RNA-seq analysis.Rmd b/vignettes/RNA-seq analysis.Rmd
@@ -411,10 +411,10 @@ contains an interaction effect).
 
 # Perform gene set enrichment analysis (GSEA)
 
-Usually, the final step in such a bioinformatics analysis is GSEA. To
-each clustered hit, the respective gene can be assigned and GSEA
-performed. For this, the Enrichr databases of choice have to be
-downloaded:
+Once the clustered hits are identified, a subsequent step to gain biological 
+insights is to perform GSEA. For this, the respective genes can be assigned to 
+each clustered hit, and GSEA can be carried out. To proceed, the Enrichr 
+databases of choice need to be downloaded:
 
 ```{r download Enrichr databases, eval = FALSE}
 # Specify which databases you want to download from Enrichr

diff --git a/vignettes/get-started.Rmd b/vignettes/get-started.Rmd
@@ -775,10 +775,10 @@ contains an interaction effect).
 
 # Perform gene set enrichment analysis (GSEA)
 
-Usually, the final step in such a bioinformatics analysis is GSEA. To
-each clustered hit, the respective gene can be assigned and GSEA
-performed. For this, the Enrichr databases of choice have to be
-downloaded:
+Once the clustered hits are identified, a subsequent step to gain biological 
+insights is to perform GSEA. For this, the respective genes can be assigned to 
+each clustered hit, and GSEA can be carried out. To proceed, the Enrichr 
+databases of choice need to be downloaded:
 
 ```{r download Enrichr databases, eval = FALSE}
 # Specify which databases you want to download from Enrichr