Analysis: CodeWAS: Viewer

[javier-gracia-tabuenca-tuni]

duplicate codes from timeCodeWas

replace module to visualize timeCodeWAS with a new module for visualize codeWAS

Visualization can take code from https://github.com/tbilab/meToolkit more info https://prod.tbilab.org/phewas_me_info/A_phewasME_in_depth_intro.html demo https://prod.tbilab.org/phewas_me/

Example of a zip with codeWAS data test_codeWAS.zip

it has 3 tables that may be used, these follow description similart to explained in https://prod.tbilab.org/phewas_me

i made these table to fit what the phewas_me may be using, these can change later, or we can make it to what we need

[javier-gracia-tabuenca-tuni]

i made the initial code only thing missing is to format the raw table

[javier-gracia-tabuenca-tuni]

there is branch 23-analysis-codewas-viewer with some changes already move to the branch launch the app import test file https://github.com/FINNGEN/CohortOperationsViewer/blob/23-analysis-codewas-viewer/tests/testthat/testdata/codeWAS/eunomia_asthmaVSasthmaControls_CodeWASSqlite.zip navigate to 'codeWAS' menu

there is the raw table

this is rendered at this point in code https://github.com/FINNGEN/CohortOperationsViewer/blob/dfcb400041c536575dd611019e67f5cae5ae4c28/R/mod_CodeWASVisualisation.R#L102

[javier-gracia-tabuenca-tuni]

TODO:

• decide what columns to show and in what order
• format the table numbers and such correctly
• links to Athena like in timeCodeWAS (concept id is calculated with covaraite id removing the last 3 digits)
• add menu with different filters , come to mind now
  • picker for analysis_name
  • picker for domain
  • covariate type, all, proportion, continuous
  • p_value (slider ?)
  • odds_ratio (slider ?)
  • Option to download the table as csv

[javier-gracia-tabuenca-tuni]

@mpreeve looking at the picture do you have more filters to add ?

[javier-gracia-tabuenca-tuni]

for reference these are the filter in CohortDiagnostics for similar data

[javier-gracia-tabuenca-tuni]

Columns in this order

• remove row number
• Database ( instead of DBid)
• Domain Name
• Analysis Name
• Covariate Name (instead of Cov Name)
• Concept Id (if id is not 0, to include a hiper link to to atlast for that code (this is how i did for timeCodeWAS https://github.com/FINNGEN/CohortOperationsViewer/blob/4186de5c4a445254b5a98b855d57ede2f09355d5/R/mod_TimeCodeWASPlot.R#L243)
• N cases (empty instead of NA)
• N Controls (empty instead of NA)
• p
• OR
• Beta
• SE
• Model
• Notes (empty instead of NA)

[javier-gracia-tabuenca-tuni]

Filters ,

• Picker Database
• Picker one or more Domains
• Picker one or more Analysis
• Picker one or more Model
• filter for p value, other than slider, maybe bins like you did in TimeCodeWAS, ?

[siirtola]

Some column names had to be shortened, but otherwise this should be working now.