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Contributing to CRI-iAtlas

Welcome, and thanks for your interest in contributing to the Cancer Research Institute (CRI) iAtlas!

If you would like to contribute code changes please follow these steps:

  1. Search the issues list in the repo. Consider opening an issue related to the suggested feature.
  2. Create a personal fork and commit new code development to personal branches in that fork.
  3. Propose changes via pull request of personal branches.

In case the intended contribution consists of a new module, please refer to the following steps to include shortcuts of new modules in the Explore Section of CRI-iAtlas.

Procedures for Starting a New iAtlas Module

Procedures to include a new module in the initial page of the Explore Section of the current version of the portal CRI-iAtlas (February 2020).

This procedure lists the files that need to be updated or started, as well as the functions to call, when applicable. There is no reference to a specific line to update, as this can change over time. It is recommended to look for the section of the code with the settings of current modules - for example, in step 4.1., at the server.R file, look for callModule code for the existing modules, and include new code in this section.

Steps

Can be carried out in another order but all pieces need to be in place for full functionality.

1. Create file with new module and save it in the modules folder : modules/myshinynewmodule.R.

2. Edit configuration.yaml.

Add the new module name in the module_files list: modules/myshinynewmodule.R

IMPORTANT: if you create a script with functions, save it in the functions folder and add the file names in the function_files list in configuration.yaml

3. In your module script myshinynewmodule.R, define the name of the UI and server function.

In this example, the names will be:

newmodule_UI <-function(id){}

newmodule <- function(input, output, session){}

Please note that this function can take more arguments.

4. Edit top level server.R.

Include a callModule for your module server function:

callModule(newmodule, moduleN, …)

Give module a number such as moduleN. Check if moduleN is unique.

Add the following in the observeEvent section:

    observeEvent(input$link_to_moduleN, {
      shinydashboard::updateTabItems(session, "explorertabs", "new_module")
    })

Observe that in 4.2., "new_module” is distinct from newmodule defined in #3.

5. Now it is time to include access to your new module in the initial page of the portal. To do so, edit pages/explorepage.R.

Add the following in the tabItem section found near bottom of this script:

tabItem(
        tabName = "new_module",
        newmodule_UI("moduleN")
      )

Add link to the left navigation bar (into code near the top of this script):

 menuSubItem(
                 "Test Module", #text to display
                 tabName = "new_module",
                 icon = icon("cog") #can be different for other sections
      )

Edit main section to include the new module in the initial Explore page:

fluidRow(
            imgLinkBox(
              width = 6,
              title = "New Module",
              linkId = "link_to_moduleN",
              imgSrc = "images/myimage.png", # if including images, read next step.
              boxText = "Short description of the module",
              linkText = "Open Module"
)

You may have to adjust layout after step 5.3.

Include a png if you like. Save the image at www/images/myimage.png.