Configuration

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 Outlier Explorer 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 the Safety Outlier Explorer 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

The sections below describe each safety-outlier-explorer setting as of version 2.3.0.

settings.id_col

string

unique identifier variable name

default: "USUBJID"

settings.time_cols

array

visit metadata

default:

[
  {
    "type": "ordinal",
    "value_col": "VISIT",
    "label": "Visit",
    "order_col": "VISITNUM",
    "order": null,
    "rotate_tick_labels": true,
    "vertical_space": 100
  },
  {
    "type": "linear",
    "value_col": "DY",
    "label": "Study Day",
    "order_col": "DY",
    "order": null,
    "rotate_tick_labels": false,
    "vertical_space": 0
  }
]

settings.time_cols[].type

string

Visit variable data type

default: "ordinal"

settings.time_cols[].value_col

string

Visit variable name

default: "VISIT"

settings.time_cols[].label

string

Visit variable label

default: "Visit"

settings.time_cols[].order_col

string

Visit ordering variable name

default: "VISITNUM"

settings.time_cols[].order

array

Visit order

default: none

settings.time_cols[].rotate_tick_labels

boolean

Rotate tick labels 45 degrees?

default: true

settings.time_cols[].vertical_space

number

Rotated tick label spacing

default: 100

settings.measure_col

string

measure variable name

default: "TEST"

settings.unit_col

string

measure unit variable name

default: "STRESU"

settings.value_col

string

result variable name

default: "STRESN"

settings.normal_col_low

string

LLN variable name

default: "STNRLO"

settings.normal_col_high

string

ULN variable name

default: "STNRHI"

settings.start_value

string

value of measure to display initially

default: none

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:

[
  {
    "value_col": "AGE",
    "label": "Age"
  },
  {
    "value_col": "SEX",
    "label": "Sex"
  },
  {
    "value_col": "RACE",
    "label": "Race"
  }
]

settings.details[].value_col

string

Variable name

default: "AGE"

settings.details[].label

string

Variable label

default: "Age"

settings.tooltip_cols

object

added in v2.4. Takes an array of col/label objects and adds those values to the end of the standard point tooltips. The following would add Date to the tooltip: {tooltip_cols: [{label:"Date",value_col:"DT"}]};

default: null

settings.multiples_sizing

object

width and height of small multiples

settings.multiples_sizing.width

number

Width

default: 300

settings.multiples_sizing.height

number

Height

default: 100

settings.normal_range_method

string

method for identifying the normal range

default: "LLN-ULN"

settings.normal_range_sd

number

the number of standard deviations from the mean with which to define the normal range

default: 1.96

settings.normal_range_quantile_low

number

this quantile defines the lower bound of the normal range

default: 0.05

settings.normal_range_quantile_high

number

this quantile defines the upper bound of the normal range

default: 0.95

settings.visits_without_data

boolean

controls display of visits without data for the current measure

default: false

settings.unscheduled_visits

boolean

controls display of unscheduled visits

default: false

settings.unscheduled_visit_pattern

string

a regular expression that identifies unscheduled visits

default: "/unscheduled|early termination/i"

settings.unscheduled_visits_values

array

an array of strings that identify unscheduled visits; overrides unscheduled_visit_pattern

default: none

settings.line_attributes

object

an object that defines the line color, thickness, and opacity

settings.line_attributes.stroke

string

Line Color

default: "black"

settings.line_attributes.stroke-width

number

Line Thickness

default: 0.5

settings.line_attributes.stroke-opacity

number

Line Opacity

default: 0.75

settings.point_attributes

object

an object that defines the point color, radius, and opacity and its outline color, thickness, and opacity

settings.point_attributes.stroke

string

Point Outline Color

default: "rgb(102,194,165)"

settings.point_attributes.stroke-width

number

Point Outline Thickness

default: 0.5

settings.point_attributes.stroke-opacity

number

Point Outline Opacity

default: 1

settings.point_attributes.fill

string

Point Color

default: "rgb(102,194,165)"

settings.point_attributes.radius

number

Point Radius

default: 3

settings.point_attributes.fill-opacity

number

Point Opacity

default: 1

Webcharts settings

The object below contains each Webcharts setting as of version 2.3.0.

{
    x: {
        column: null, //set in syncSettings()
        type: null, //set in syncSettings()
        behavior: 'raw'
    },
    y: {
        column: null, //set in syncSettings()
        stat: 'mean',
        type: 'linear',
        label: 'Value',
        behavior: 'raw',
        format: '0.2f'
    },
    marks: [
        {
            per: null, //set in syncSettings()
            type: 'line',
            attributes: {
                'clip-path': 'url(#1)'
            },
            tooltip: null //set in syncSettings()
        },
        {
            per: null, //set in syncSettings()
            type: 'circle',
            attributes: {
                'clip-path': 'url(#1)'
            },
            tooltip: null //set in syncSettings()
        }
    ],
    resizable: true,
    margin: { right: 20 }, //create space for box plot
    aspect: 3
}