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OmopViewer

The goal of OmopViewer is to allow the user to easily create Shiny Apps to visualise study results in <summarised_result> format.

Installation

Install it from cran:

install.packages("OmopViewer")

Or you can install the development version of OmopViewer from GitHub with:

install.packages("pak")
pak::pkg_install("OHDSI/OmopViewer")

Main functionalities

The package has two functionalities:

  • Static app
  • Dynamic app

Static shiny app

The static shiny app functionality creates a static shiny from a list of summarised_result objects. This shiny is specific to the set of results and can be modified later locally.

# lets generate some results
library(CohortCharacteristics)
#> Registered S3 method overwritten by 'visOmopResults':
#>   method                 from        
#>   tidy.summarised_result omopgenerics
cdm <- mockCohortCharacteristics()
#> Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable',
#>  target signature 'duckdb_connection#Id'.
#>  "duckdb_connection#ANY" would also be valid
result <- summariseCharacteristics(cdm$cohort1) |>
  bind(summariseCohortAttrition(cdm$cohort1))
#> ℹ adding demographics columns
#> ℹ summarising data
#> ✔ summariseCharacteristics finished!
#> `cohort_definition_id` casted to character.

exportStaticApp(result = result, directory = tempdir())
#> ℹ Processing data
#> ✔ Data processed: 2 panels idenfied: `summarise_characteristics` and
#>   `summarise_cohort_attrition`.
#> ℹ Creating shiny from provided data
#> `cohort_definition_id` eliminated from settings as all elements are NA.
#> ✔ Shiny created in:
#>   /var/folders/pl/k11lm9710hlgl02nvzx4z9wr0000gp/T//RtmpYP9P88/shiny

This function allow some customisation of the shiny with the arguments:

  • theme (to choose a pre-built theme or a bslib one).
  • logo (you can point to one of the pre-builr logos or to a local image).
  • title
  • background whether to allow for an .md file for customisation of a background panel.
  • summary whether to include or not a summary panel.
  • panelStructure allows you to structure the different panels in dropdown menus.
  • panelDetails allows you to create panels at result_id level and assign which are the outputs that we want to include in each panel.

The shiny generated will have the following structure:

  • global.R loads the data.
  • ui.R with all the ui code. You can edit there the buttons and its default values.
  • server.R server logic, you can edit that file to change some of the displays.
  • functions.R some utility functions that are used in the shiny app.
  • data/result.csv the original summarised_result provided.
  • data/ShinyData.RData the .RData file that contains the data used in the shiny.
  • data/preprocess.R the file to generate ShinyData.RData from results.csv

Dynamic shiny app

The dynamic shiny app can be easily launched with launchDynamicApp() function. This function creates a shinyApp where you can upload multiple results sets and visualise them.

By default the shiny generated will have no data, you have to upload data from a csv or zip file that you have it locally. The summarised_results will be processed and you will be allowed to choose which results to visualise.