Configuration

Configuration Overview

The most straightforward way to customize the Safety Outlier Explorer is by using a configuration object whose properties describe the behavior and appearance of the chart. Since the safety eDish is a Webcharts chart object, many default Webcharts settings are set in the defaultSettings.js file as described below. Refer to the Webcharts documentation for more details on these settings.

In addition to the standard Webcharts settings several custom settings not available in the base Webcharts library have been added to facilitate data mapping and other custom functionality. These custom settings are described in detail below. All defaults can be overwritten by users.

Renderer-specific settings

settings.id_col

string

unique identifier variable name

default: "USUBJID"

settings.value_col

string

result variable name

default: "STRESN"

settings.measure_col

string

measure variable name

default: "TEST"

settings.unit_col

string

measure unit variable name

default: "STRESU"

settings.normal_col_low

string

LLN variable name

default: "STNRLO"

settings.normal_col_high

string

ULN variable name

default: "STNRHI"

settings.visitn_col

string

Visit number variable name

default: "VISITN"

settings.visitn_col

string

Visit number variable name

default: "VISITN"

settings.baseline_visitn

string

Value of baseline visit number. Used to calculate mDish.

default: "1"

settings.filters

array

an array of filter variables and associated metadata

default: none

settings.filters[].value_col

string

Variable name

default: none

settings.filters[].label

string

Variable label

default: none

settings.details

array

an array of ID-level variables and associated metadata

default: Automatically uses values specified in settings.id_col, settings.group_cols and settings.filters

settings.details[].value_col

string

Variable name

default: Automatically uses values specified in settings.id_col, settings.group_cols and settings.filters

settings.details[].label

string

Variable label

default: Automatically uses values specified in settings.id_col, settings.group_cols and settings.filters

settings.group_cols

array

an array of grouping variables and associated metadata

default: none

settings.group_cols[].value_col

string

Variable name

default: none

settings.group_cols[].label

string

Variable label

default: none

settings.measure_details

array

An array defining key properties of the lab measures used in eDish evaluations.

default:

[
        {
            label: 'ALT',
            measure: 'Aminotransferase, alanine (ALT)',
            axis: 'x',
            imputation: 'data-driven',
            cut: {
                relative_baseline: 3.8,
                relative_uln: 3,
                absolute: 1.0
            }
        },
        {
            label: 'ALP',
            measure: 'Alkaline phosphatase (ALP)',
            axis: null,
            imputation: 'data-driven',
            cut: {
                relative_baseline: 3.8,
                relative_uln: 1,
                absolute: 1.0
            }
        },
        {
            label: 'TB',
            measure: 'Total Bilirubin',
            axis: 'y',
            imputation: 'data-driven',
            cut: {
                relative_baseline: 4.8,
                relative_uln: 2,
                absolute: 40
            }
        }
    ]

settings.measure_details[].label

string

short text label for the measure

default: see settings.measure_details

settings.measure_details[].measure

string

Long text label for the measure, used as label for chart axis

default: see settings.measure_details

settings.measure_details[].axis

string

Specifies whether the measure should be displayed on the x or y axis in the eDish scatter plot. Valid options are "x" and "y" and null. Note that measures with no axis value (or null) specified, are not shown in the eDish scatter plot, but are included in participant summaries opened by clicking points on the scatter plot.

default: "x" for "Aminotransferase, alanine (ALT)" and "y" for "Total Bilirubin", null otherwise as shown in settings.measure_details

settings.measure_details[].imputation

string

specified how data should be imputed for the specified measure. Valid options are:

• "data-driven" is the default and it takes 0 values and sets them to 0.5 times the minimum value for the measure across all participants/time points
• "user-defined" takes all values less than measure_details.imputation_value and sets then to 0.5 times measure_details.imputation_value. (The imputation_value option is ignored otherwise)
• "drop" means all 0 values are dropped.

default: "data-driven"

settings.measure_details[].imputation_value

number

used as described above when settings.measure_details.imputation is set to "user-defined"

default: none

settings.measure_details[].cut

object

Object defining default cut-points for the 3 different types of supported eDish displays

default: see settings.measure_details

settings.measure_details[].cut.relative_baseline

number

Default cut point used for the given measure when viewing mDish (settings.display == "relative_baseline")

default: see settings.measure_details

settings.measure_details[].cut.relative_uln

number

Default cut point used for the given measure when viewing standard eDish (settings.display == "relative_ULN")

default: see settings.measure_details

settings.measure_details[].cut.absolute

number

Default cut point used for the given measure when viewing absolute values (settings.display == "absolute")

default: see settings.measure_details

settings.display

"string"

Defines the display type used on the eDish scatter plot on initial view. Can be changed by the user once the chart is rendered. Valid options are:

• "relative_uln" which shows the standard eDish view where values are scaled relative to the Upper Limit or Normal
• "relative_baseline" which shows the mDish view where values are scaled relative to the participants baseline value
• "absolute" which show the raw values for the measure

settings.axis_options

array

Defines nice labels for the different display options.

default:

  axis_options: [
        { label: 'Upper limit of normal adjusted (eDish)', value: 'relative_uln' },
        { label: 'Baseline adjusted (mDish)', value: 'relative_baseline' },
        { label: 'Raw Values', value: 'absolute' }
    ]

settings.measureBounds

array of number

Sets upper and lower percentiles used for defining outlier in the "Lab Summary Table" in the participant details section.

default: [0.01,0.99]

settings.populationProfileURL

string

URL linking to additional charts related to population level analysis

default: none

settings.participantProfileURL

string

URL linking to additional charts related to population level analysis. Will need an update in a future release to allow dynamic links for different participants.

default: none

settings.visit_window

number

Default visit window used to highlight eDish points where x and y measures occurred within the specified number of days. Editable by user after render.

default: 30

settings.point_size

string

Option to change point size based on a key variable. Can be set to any value defined in settings.measure_variables[].label. No custom point size is used when the option is set to "uniform" (the default).

default: "uniform"

Webcharts settings

The object below contains the default Webcharts settings for the display.

  x: {
        column: null, //set in onPreprocess/updateAxisSettings
        label: null, // set in onPreprocess/updateAxisSettings,
        type: 'linear',
        behavior: 'raw',
        format: '.2f'
        //domain: [0, null]
    },
    y: {
        column: null, // set in onPreprocess/updateAxisSettings,
        label: null, // set in onPreprocess/updateAxisSettings,
        type: 'linear',
        behavior: 'raw',
        format: '.2f'
        //domain: [0, null]
    },
    marks: [
        {
            per: [], // set in syncSettings()
            type: 'circle',
            summarizeY: 'mean',
            summarizeX: 'mean',
            attributes: { 'fill-opacity': 0 }
        }
    ],
    gridlines: 'xy',
    color_by: null, //set in syncSettings
    max_width: 900,
    aspect: 1,
    legend: { location: 'top' },
    margin: { right: 25, top: 25, bottom: 75 }