Moved R options to the top of image_data_explorer.R. Updated README.

README.md

@@ -44,10 +44,10 @@ Download the code from the project's repository and run it from within the proje
 ```
 > git clone git@git.embl.de:meechan/image-data-explorer.git
 > cd image-data-explorer
-> Rscript image_data_explorer.R
+> R -e 'shiny::runApp("image_data_explorer.R", host = "0.0.0.0", port = 5476)'
 ```
 The app is then accessible from a web browser at http://127.0.0.1:5476  
-Alternatively, open the file image_data_explorer.R with [RStudio](https://www.rstudio.com/products/rstudio/download/). Set the working directory to the app directory (i.e. image-data-explorer) to allow building the app image viewer then click the 'Run App' button.
+Alternatively, open the file image_data_explorer.R with [RStudio](https://www.rstudio.com/products/rstudio/download/) then click the 'Run App' button.
 
 #### Building and running as a container
 Download and install [Docker](https://docs.docker.com/get-docker/). On Windows, make sure that Docker Desktop uses the Windows Subsystem for Linux 2 (WSL2). Then clone this repository.  

image_data_explorer.R

@@ -4,6 +4,12 @@
 ## Main application file ##
 ###########################
 
+# Increase max upload size to 500 MB
+options(shiny.maxRequestSize=500*1024^2)
+
+## Increase amount of RAM allocated to the JVM to allow BioFormats to read large files. This needs to be done before loading rJava (or packages using it).
+# options(java.parameters = "-Xmx8g") 
+
 ## Install required packages if missing
 ## CRAN packages
 pkg <- c("devtools", "BiocManager", "DT", "shiny", "shinyFiles", "shinycssloaders", "shinydashboard", "shinyjs", "shinyWidgets", "shinybusy", "assertthat", "ggplot2", "plotly", "RANN", "MASS", "uwot")
@@ -41,12 +47,6 @@ library(RANN)
 library(MASS)
 library(uwot)
 
-# Increase max upload size to 500 MB
-options(shiny.maxRequestSize=500*1024^2)
-
-## Increase amount of RAM allocated to the JVM to allow BioFormats to read large files.
-# options(java.parameters = "-Xmx8g" ) 
-
 ## Making data table filtering persistent
 ## from https://dev.to/awwsmm/reactive-datatables-in-r-with-persistent-filters-l26
 ## Default global search value