diff --git a/inst/rmarkdown/index.Rmd b/inst/rmarkdown/index.Rmd index f4e42ac..abdaf4a 100644 --- a/inst/rmarkdown/index.Rmd +++ b/inst/rmarkdown/index.Rmd @@ -27,6 +27,11 @@ params: library(knitr) options(width=400) scigenex::set_verbosity(0) + +# Disable tutorial exercise checking to prevent chunks ending in +# '-check' from being interpreted as learnr exercise check chunks +options(tutorial.exercise.checker = NULL) + knitr::opts_chunk$set( fig.path="all_", fig.align = "center", diff --git a/inst/rmarkdown/module.Rmd b/inst/rmarkdown/module.Rmd index 0bf914c..5ff2242 100644 --- a/inst/rmarkdown/module.Rmd +++ b/inst/rmarkdown/module.Rmd @@ -23,6 +23,10 @@ scigenex::set_verbosity(0) library(knitr) options(width=400) +# Disable tutorial exercise checking to prevent chunks ending in +# '-check' from being interpreted as learnr exercise check chunks +options(tutorial.exercise.checker = NULL) + knitr::opts_chunk$set( fig.path="FIG_PATH", fig.align = "center", diff --git a/vignettes/report.Rmd b/vignettes/report.Rmd index aa5b042..3048866 100644 --- a/vignettes/report.Rmd +++ b/vignettes/report.Rmd @@ -9,6 +9,12 @@ vignette: > %\usepackage[UTF-8]{inputenc} --- +```{r setup, include=FALSE} +# Disable tutorial exercise checking to prevent any chunks ending in +# '-check' from being interpreted as learnr exercise check chunks +options(tutorial.exercise.checker = NULL) +knitr::opts_chunk$set(echo = TRUE) +``` ## Introduction diff --git a/vignettes/spatial.Rmd b/vignettes/spatial.Rmd index a955e81..9d2b7c0 100644 --- a/vignettes/spatial.Rmd +++ b/vignettes/spatial.Rmd @@ -9,6 +9,13 @@ vignette: > %\usepackage[UTF-8]{inputenc} --- +```{r setup, include=FALSE} +# Disable tutorial exercise checking to prevent any chunks ending in +# '-check' from being interpreted as learnr exercise check chunks +options(tutorial.exercise.checker = NULL) +knitr::opts_chunk$set(echo = TRUE) +``` + ## Working with spatial transcriptomics datasets The scigenex package offers a certain number of functions dedicated to spatial transcriptomic data analysis. At the moment these functions have been mainly developed to analyse VISIUM technology (10X Genomics). diff --git a/vignettes/usage.Rmd b/vignettes/usage.Rmd index 2a81c90..21ac6b8 100644 --- a/vignettes/usage.Rmd +++ b/vignettes/usage.Rmd @@ -9,6 +9,13 @@ vignette: > %\usepackage[UTF-8]{inputenc} --- +```{r setup, include=FALSE} +# Disable tutorial exercise checking to prevent any chunks ending in +# '-check' from being interpreted as learnr exercise check chunks +options(tutorial.exercise.checker = NULL) +knitr::opts_chunk$set(echo = TRUE) +``` + # Guided tutorial The easiest way to use scigenex is to perform the following steps using the Seurat R package: