safetyOutlierExplorer and safetyResultsOverTime widgets initialization

[xni7]

@jwildfire , I tried an ADaM dataset with AVISIT and AVISITN columns, but couldn't render safetyOutlierExplorer or safetyResultsOverTime widgets. The value "VISIT" for the this.config.x.column setting does not match any column in the provided dataset.

After referring to their JS Data Guidelines, two widgets requires other metadata/mapping than visit_col and visitn_col.

• outlier widget: time_cols
• boxplot widget: time_settings

Two considerations

• Add a test for ADaM data with AVISIT and AVISITN only, e.g. tests/testthat/module_examples/chartsRenderWidget/app.R. I added a safetyOutlierExplorer widget and additional mapping and got it rendered.

mappingLabs$time_cols <- data.frame(
  value_col = c("AVISIT", "ADY"),
  type = c("ordinal", "linear"),
  order_col = c("AVISITN" , "null"),
  rotate_tick_labels = c(T,F),
  vertical_space = c(100,0)
)

• Add widget init function in config/workflow. The Chart Config Vignette is really helpful! I followed the aeExplorer_init() example and created a custom workflow for safetyOutlierExplorer_init() function and added to its YAML. It worked like a charm!

safetyOutlierExplorer_init<- function(data, settings){
    print(data)
    print(settings)
    
    settings$time_cols <- data_frame(
        value_col = c(settings[["visit_col"]], settings[["studyday_col"]]),
        type = c("ordinal", "linear"),
        order_col = c(settings[["visitn_col"]] , "null"),
        rotate_tick_labels = c(T,F),
        vertical_space = c(100,0)
    )
    
    return(list(data=data,settings=settings))
}

Comments

• I think the widget initialization is "hidden" in the code backend, and users need to familiar with the JavaScript Data Specifications. It will be challenging for non technical users.
• Some of the widget JS settings are not in the meta data, perhaps consider some chart specific control UIs using Shiny on those charts?

[xni7]

Can also rename AVISIT/AVISITN to VISIT/VISITNUM and use the default settings, or add more widgets settings to the meta data table?

[jwildfire]

Nice write-up, @xni7! I'm really glad you could work through this bug the init function and test infrastructure. Moving forward, I think your last comment is the most straightforward way to fix the issue.

Can also rename AVISIT/AVISITN to VISIT/VISITNUM and use the default settings, or add more widgets settings to the meta data table?

Yes! I'll put in a quick PR that updates meta with the correct Adam column names, and hopefully that will fix things for this use case.

[jwildfire]

• I think the widget initialization is "hidden" in the code backend, and users need to familiar with the JavaScript Data Specifications. It will be challenging for non technical users.
• Some of the widget JS settings are not in the meta data, perhaps consider some chart specific control UIs using Shiny on those charts?

Yeah, I hear you. I do think that building shiny module "wrappers" that allow for additional customization of some of the more complex widgets is a good option down the road. Also no reason we can't create some {safetyexploreR} style wrapper functions with more robust parameterization in {safetyCharts} down the road. My plan was wait and see what users ask for before putting in too much work on this front, but certainly open to discussion.

Will close this issue once the metadata is fixed, but might be worth spinning the larger discussion of how the widgets are parameterized off in to a discuss topic

[jwildfire]

@xni7 I also would've thought you could just update the columns in the mapping tab ... was that not working as expected?