Commit e11394c5 authored by Jean-Karim Heriche's avatar Jean-Karim Heriche

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

parent a5c93fa3
......@@ -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.
......
......@@ -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
......
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