GWAS_locus_browser

• updated 5/13/2021

Contributors

• Main Developers: Francis P. Grenn, Jonggeol J. Kim, Mary B. Makarious
• Design and Concept: Francis P. Grenn, Jonggeol J. Kim, Mary B. Makarious, Cornelis Blauwendraat, Andrew B. Singleton

Package Versions

R version 4.2.1
data.table/1.14.2
dplyr/1.0.10
DT/0.24
ggplot2/3.3.6
googleAnalyticsR/1.1.0
googledrive/2.0.0
htmlwidgets/1.5.4
httr/1.4.4
openxlsx/4.2.5.2
plotly/4.9.3
shiny/1.6.0
shinyanimate/0.3.0
shinycssloaders/1.0.0
shinydashboard/0.7.2
shinydashboardPlus/0.7.5
shinyhelper/0.3.2
shinyjs/2.1.0
shinyWidgets/0.5.0
stringr/1.4.1

File Overview

• ui.R - code for user interface layout.
• server.R - code for server logic.
• global.R - library imports and code to call other R files. Make changes to this file if you are adding a new section to the browser.
• sidebar.R - code for the sidebar and header elements. Contains logic for the searchbar.
• tutorial.R - code for the tutorial mode.
• about.R - code for the about tab.
• user_stats.R - code for the user stats tab.
• [name]_section.R - code for a section in the browser.
• appManifest.txt - list of files and folders that will be deployed to the server for the public version of the app
  • typically includes: all .R files, the www/ folder
• DataProcessing - contains all scripts used to filter and clean the data for the app
• www - contains all the data (tables and images) that will be displayed in the app

Making Changes

Some general steps to follow if you are adding new data to the browser.

• 1) Adding a new section (one of the collapseable/expandable parts with tables, images, etc) to the data tab of the browser.

• 2) Adding new variants from an exisitng GWAS. (WIP)

• 3) Adding new data to the evidence per gene table. (WIP)

1) Adding a New Section to the Data Tab

a) Make a New Section R File

Make a new R file (something like [name]_section.R).

Some simple examples are burden_section.R,pheno_vars_section.R,etc...

The R file will need the following for it to work in the browser:

• (i) start with a list that will contain variables and functions for the new section.

  • (ii)-(vii) must all be added to this list

  newSection<-list()

• (ii) add an id to the list

  • this will be used to identify the section when using the "jump to section" drop down.
  • this will also be used to identify the correct help markdown file for the section.

  newSection$id <- "newsection"

• (iii) add a title to the list

  • this is the title that will be displayed for the section in the browser.

  newSection$title <- "New Section Title"

• (iv) add a loadData function to the list

  • this function should contain code to read data and create dataframes. Variable, dataframes, etc, that will be displayed in the browser should be initilized using <<- (not <-).
  • Input: None.
  • Output: No return values needed.

  newSection$loadData<- function(){
    new_section_data <<- fread("www/newSectionDataFile.csv")
  }

• (v) add a generateUI function to the list

  • this function will create the user interface for the section, excluding the accordion and help button.
  • Input: None.
  • Output: Return all of the user interface code in a div, fluidRow, etc.

  newSections$generateUI<- function(){
    fluidRow(
      column(dataTableOutput("newSectionTable"), width = 12)
    )
  }

• (vi) add a serverLogic function to the list

  • this function will contain all server logic code. This is where the outputs are rendered and changes to inputs are observed.
  • Input: input, output and session objects from the server
  • Output: None.

  newSection$serverLogic <- function(input,output,session)
  {
    #code here to render outputs, observe inputs, etc...
  }

• (vii) can add other functions if necessary

  • qtl_section.R, for example, has extra functions added to its lists to allow it to communicate with the evidence_section.R code.

b) Add the New Section File to global.R

• add code to reference the new R file

source("new_section.R",local=T)

• add the list from the R file to the sections list

sections <- list(locusZoom=locusZoom,newSection=newSection)

c) Add a Help Markdown File

• must be named after the section's id
• the help markdowns go in www/help_files/

d) Update Documentation

• update the version number in global.R
• update the version and document the changes in the file used in the about tab.

e) Update appManifest.txt

• add new R files to the appManifest.txt so they will be picked up when deploying the app.

2) Adding New Variants from an Exisitng GWAS. (WIP)

• See the DataProcessing directory for steps on which scripts to run.