feat: add docs auto-linking & code folding in R Markdown reports

CHANGELOG.md

@@ -1,6 +1,10 @@
 ## SINCLAIR development version
 
 - Set main job memory to 2 GB for slurm mode. (#205, @kelly-sovacool)
+- Improvements to R Markdown reports: (#216, @kelly-sovacool)
+    - Link to function documentation websites.
+    - Use code folding to include code in output, but set it to 'hide' by default.
+    - Hide R messages by default.
 
 ## SINCLAIR 0.3.5
 

bin/batch_correction_cca.Rmd

@@ -1,8 +1,12 @@
 ---
 title: "Batch Correction: CCA"
-author: "Samantha Sevilla"
+author: "CCR Collaborative Bioinformatics Resource"
 date: "`r Sys.Date()`"
-output: html_document
+output:
+  html_document:
+    toc: true
+    code_folding: hide
+    downlit_highlight: true
 editor_options:
   chunk_output_type: console
 params:
@@ -17,9 +21,14 @@ params:
   scRNA_functions: "/data/CCBR_Pipeliner/Pipelines/SINCLAIR/dev/bin/scRNA_functions.R"
   testing: "Y"
 ---
+```{r, setup, include=FALSE}
+knitr::opts_chunk$set(
+  message = FALSE,
+  echo = TRUE
+)
+```
 
-
-```{r, prep_args,  message=FALSE}
+```{r, prep_args}
 # set up params
 species <- params$species
 gid <- params$gid
@@ -38,7 +47,7 @@ testing <- params$testing
 scRNA_functions <- params$scRNA_functions
 ```
 
-```{r, handle_pkg, message=FALSE}
+```{r, handle_pkg}
 # source functions
 source(scRNA_functions)
 
@@ -62,7 +71,7 @@ scRNA_handle_packages(pkg_df)
 options(future.globals.maxSize = 96000 * 1024^2)
 ```
 
-```{r, processing, message=FALSE}
+```{r, processing}
 # read in merged object
 so <- readRDS(mergedObj)
 
@@ -78,7 +87,7 @@ so_corrected <- MAIN_BATCH_CORRECTION(so, npcs, species, resolution,
 )
 ```
 
-```{r saveoutputs, message=FALSE, include=FALSE, echo=FALSE}
+```{r saveoutputs include=FALSE}
 fpath <- paste0(gid, "_batch_correction_cca.rds")
 saveRDS(so_corrected, fpath)
 ```

bin/batch_correction_harmony.Rmd

@@ -1,8 +1,12 @@
 ---
 title: "Batch Correction: Harmony"
-author: "Samantha Sevilla"
+author: "CCR Collaborative Bioinformatics Resource"
 date: "`r Sys.Date()`"
-output: html_document
+output:
+  html_document:
+    toc: true
+    code_folding: hide
+    downlit_highlight: true
 editor_options:
   chunk_output_type: console
 params:
@@ -17,8 +21,13 @@ params:
   scRNA_functions: "/data/CCBR_Pipeliner/Pipelines/SINCLAIR/dev/bin/scRNA_functions.R"
   testing: "Y"
 ---
-
-```{r, prep_args,  message=FALSE, echo=FALSE, include=FALSE}
+```{r, setup, include=FALSE}
+knitr::opts_chunk$set(
+  message = FALSE,
+  echo = TRUE
+)
+```
+```{r, prep_args, include=FALSE}
 # set up params
 species <- params$species
 gid <- params$gid
@@ -36,7 +45,7 @@ Rpkg_config <- params$Rpkg_config
 scRNA_functions <- params$scRNA_functions
 ```
 
-```{r, handle_pkg, message=FALSE}
+```{r, handle_pkg}
 # source functions
 source(scRNA_functions)
 
@@ -60,7 +69,7 @@ scRNA_handle_packages(pkg_df)
 options(future.globals.maxSize = 96000 * 1024^2)
 ```
 
-```{r, processing, message=FALSE}
+```{r, processing}
 # read in merged object
 so <- readRDS(mergedObj)
 
@@ -76,7 +85,7 @@ so_corrected <- MAIN_BATCH_CORRECTION(so, npcs, species, resolution,
 )
 ```
 
-```{r saveoutputs, message=FALSE, include=FALSE, echo=FALSE}
+```{r saveoutputs include=FALSE}
 fpath <- paste0(gid, "_batch_correction_harmony.rds")
 saveRDS(so_corrected, fpath)
 ```

bin/batch_correction_integration.Rmd

@@ -1,8 +1,12 @@
 ---
 title: "Batch Correction Analysis"
-author: "CCBR"
-date: '`r format(Sys.time(), "%a %b %d %Y - %X")`'
-output: html_document
+author: "CCR Collaborative Bioinformatics Resource"
+date: "`r Sys.Date()`"
+output:
+  html_document:
+    toc: true
+    code_folding: hide
+    downlit_highlight: true
 editor_options:
   chunk_output_type: console
 always_allow_html: true
@@ -23,8 +27,13 @@ params:
   scRNA_functions: "/data/CCBR_Pipeliner/Pipelines/SINCLAIR/dev/bin/scRNA_functions.R"
   testing: "Y"
 ---
-
-```{r, prep_args,  message=FALSE, echo=FALSE, include=FALSE}
+```{r, setup, include=FALSE}
+knitr::opts_chunk$set(
+  message = FALSE,
+  echo = TRUE
+)
+```
+```{r, prep_args, include=FALSE}
 # set up params
 # species= params$species
 gid <- params$gid
@@ -51,7 +60,7 @@ unlink(tmp_images, recursive = TRUE)
 dir.create(file.path("tmp_images"), showWarnings = FALSE)
 ```
 
-```{r, handle_pkg, message=FALSE, echo=FALSE, include=FALSE}
+```{r, handle_pkg  include=FALSE}
 # source functions
 source(scRNA_functions)
 
@@ -71,7 +80,7 @@ pkg_df
 scRNA_handle_packages(pkg_df)
 ```
 
-```{r, processing, message=FALSE, echo=FALSE, include=FALSE}
+```{r, processing  include=FALSE}
 # read in merged objects
 so_merged <- readRDS(mergedObj)
 so_rpca <- readRDS(rpcaObj)
@@ -89,7 +98,7 @@ objList <- c("merged", "rpca", "integrated", "harmony", "liger")
 
 ### Samples
 
-```{r sampleBatchCorrection, echo=FALSE, fig.width=15, fig.height=15}
+```{r sampleBatchCorrection, fig.width=15, fig.height=15}
 # plot
 plot_list_s <- list()
 
@@ -123,7 +132,7 @@ annotate_figure(p,
 
 ### Groups
 
-```{r groupBatchCorrection, echo=FALSE, fig.width=15, fig.height=15}
+```{r groupBatchCorrection, fig.width=15, fig.height=15}
 plot_list_g <- list()
 for (i in 1:length(objList)) {
   obj <- OBJECT_SELECT(objList[i])
@@ -150,7 +159,7 @@ annotate_figure(p,
 
 ### Cell type annotations
 
-```{r annotationBatchCorrection, echo=FALSE, fig.width=15, fig.height=15}
+```{r annotationBatchCorrection, fig.width=15, fig.height=15}
 plot_list_annot <- list()
 for (i in 1:length(objList)) {
   obj <- OBJECT_SELECT(objList[i])
@@ -187,7 +196,7 @@ DT::datatable(
 
 ### RPCA
 
-```{r, echo=FALSE,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
+```{r,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
 method <- "rpca"
 files <- list.files(
   path = tmp_images,
@@ -203,7 +212,7 @@ if (length(files) > 0) {
 
 ### ccaIntegrated
 
-```{r, echo=FALSE,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
+```{r,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
 method <- "int"
 files <- list.files(
   path = tmp_images,
@@ -219,7 +228,7 @@ if (length(files) > 0) {
 
 ### Harmony
 
-```{r, echo=FALSE,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
+```{r,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
 method <- "harmony"
 files <- list.files(
   path = tmp_images,
@@ -237,7 +246,7 @@ if (length(files) > 0) {
 
 ### scvi
 
-```{r, echo=FALSE,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
+```{r,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
 method <- "scvi"
 files <- list.files(
   path = tmp_images,
@@ -255,7 +264,7 @@ if (length(files) > 0) {
 
 ### liger
 
-```{r, echo=FALSE,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
+```{r,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
 method <- "liger"
 files <- list.files(
   path = tmp_images,
@@ -271,7 +280,7 @@ if (length(files) > 0) {
 
 ## Silhouette scores  {.tabset}
 
-```{r silhouetteImages,   message=FALSE, echo=FALSE, include=FALSE}
+```{r silhouetteImages,   , include=FALSE}
 # create matrix
 resSil_merged <- matrix(ncol = 2, nrow = length(resolution))
 resSil_merged[] <- 0
@@ -412,7 +421,7 @@ for (i in 1:length(objList)) {
 
 ### RPCA
 
-```{r, echo=FALSE,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
+```{r,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
 method <- "rpca"
 files <- list.files(
   path = tmp_images,
@@ -428,7 +437,7 @@ if (length(files) > 0) {
 
 ### ccaIntegrated
 
-```{r, echo=FALSE,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
+```{r,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
 method <- "int"
 files <- list.files(
   path = tmp_images,
@@ -444,7 +453,7 @@ if (length(files) > 0) {
 
 ### Harmony
 
-```{r, echo=FALSE,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
+```{r,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
 method <- "harmony"
 files <- list.files(
   path = tmp_images,
@@ -462,7 +471,7 @@ if (length(files) > 0) {
 
 ### scvi
 
-```{r, echo=FALSE,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
+```{r,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
 method <- "scvi"
 files <- list.files(
   path = tmp_images,
@@ -480,7 +489,7 @@ if (length(files) > 0) {
 
 ### liger
 
-```{r, echo=FALSE,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
+```{r,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
 method <- "liger"
 files <- list.files(
   path = tmp_images,

bin/batch_correction_liger.Rmd

@@ -1,8 +1,12 @@
 ---
 title: 'Batch Correction: LIGER'
-author: "Samantha Sevilla"
+author: "CCR Collaborative Bioinformatics Resource"
 date: "`r Sys.Date()`"
-output: html_document
+output:
+  html_document:
+    toc: true
+    code_folding: hide
+    downlit_highlight: true
 editor_options:
   chunk_output_type: console
 params:
@@ -17,9 +21,14 @@ params:
   scRNA_functions: "/data/CCBR_Pipeliner/Pipelines/SINCLAIR/dev/bin/scRNA_functions.R"
   testing: "Y"
 ---
+```{r, setup, include=FALSE}
+knitr::opts_chunk$set(
+  message = FALSE,
+  echo = TRUE
+)
+```
 
-
-```{r, prep_args,  message=FALSE}
+```{r, prep_args}
 # set up params
 species <- params$species
 gid <- params$gid
@@ -38,7 +47,7 @@ testing <- params$testing
 scRNA_functions <- params$scRNA_functions
 ```
 
-```{r, handle_pkg, message=FALSE}
+```{r, handle_pkg}
 # source functions
 source(scRNA_functions)
 
@@ -62,7 +71,7 @@ scRNA_handle_packages(pkg_df)
 options(future.globals.maxSize = 96000 * 1024^2)
 ```
 
-```{r, processing, message=FALSE}
+```{r, processing}
 # read in merged object
 so <- readRDS(mergedObj)
 
@@ -78,7 +87,7 @@ so_corrected <- MAIN_BATCH_CORRECTION(so, npcs, species, resolution,
 )
 ```
 
-```{r saveoutputs, message=FALSE, include=FALSE, echo=FALSE}
+```{r saveoutputs include=FALSE}
 fpath <- paste0(gid, "_batch_correction_liger.rds")
 saveRDS(so_corrected, fpath)
 ```