Module: LocusZoom_ScaleFunctions

Plugin registry of available functions that can be used in scalable layout directives.

These "scale functions" are used during rendering to return output (eg color) based on input value

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Methods

(inner) categorical_bin(parameters)

Function to sort values of any type into bins based on direct equality testing with a list of categories. Will return null if provided an input value that does not match to a listed category.

Parameters:
Name Type Description
parameters Object
Properties
Name Type Description
categories Array

Array of values against which to evaluate the input value. Must be of equal length to values parameter. If the input value is equal to category n then returned value is the nth entry in the values parameter.
values Array

Array of values to return given evaluations against categories. Must be of equal length to categories parameter. Each entry n represents the value to return if the input value is equal to the nth value in the categories parameter.
null_value *

Value to return if the input value fails to match to any categories. Optional.
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(inner) effect_direction(parameters, input) → {null}

Calculate the effect direction based on beta, or the combination of beta and standard error. Typically used with phewas plots, to show point shape based on the beta and stderr_beta fields.

Parameters:
Name Type Description
parameters
Properties
Name Type Description
'+'

The value to return if the effect direction is positive
'-'

The value to return if the effect direction is positive
beta_field

The name of the field containing beta
stderr_beta_field

The name of the field containing stderr_beta
input Object

This function should receive the entire datum object, rather than one single field
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Returns:
Type
null

(inner) if(parameters, value)

Basic conditional function to evaluate the value of the input field and return based on equality.

Parameters:
Name Type Description
parameters Object
Properties
Name Type Description
field_value *

The value against which to test the input value.
then *

The value to return if the input value matches the field value
else *

The value to return if the input value does not match the field value. Optional. If not defined this scale function will return null (or value of null_value parameter, if defined) when input value fails to match field_value.
value *

value
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(inner) interpolate()

Function for continuous interpolation of numerical values along a gradient with arbitrarily many break points.

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(inner) numerical_bin(parameters, value) → {*}

Function to sort numerical values into bins based on numerical break points. Will only operate on numbers and return null (or value of null_value parameter, if defined) if provided a non-numeric input value. Parameters:

Parameters:
Name Type Description
parameters Object
Properties
Name Type Description
breaks Array.<Number>

Array of numerical break points against which to evaluate the input value. Must be of equal length to values parameter. If the input value is greater than or equal to break n and less than or equal to break n+1 (or break n+1 doesn't exist) then returned value is the nth entry in the values parameter.
values Array

Array of values to return given evaluations against break points. Must be of equal length to breaks parameter. Each entry n represents the value to return if the input value is greater than or equal to break n and less than or equal to break n+1 (or break n+1 doesn't exist).
null_value *
value *

value
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Returns:
Type
*

(inner) ordinal_cycle(parameters) → {*}

Cycle through a set of options, so that the each element in a set of data receives a value different than the element before it. For example: "use this palette of 10 colors to visually distinguish 100 adjacent items" This is useful when ADJACENT items must be guaranteed to yield a different result, but it leads to unstable color choices if the user pans to a region with a different number/order of items. (the same item is assigned a different color)

See also: stable_choice.

Parameters:
Name Type Description
parameters Object
Properties
Name Type Description
values Array

A list of option values
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Returns:
Type
*

(inner) stable_choice(parameters, value, index)

A scale function that auto-chooses something (like color) from a preset scheme, and makes the same choice every time given the same value, regardless of ordering or what other data is in the region

This is useful when categories must be stable (same color, every time). But sometimes it will assign adjacent values the same color due to hash collisions.

For performance reasons, this is memoized once per instance. Eg, each scalable color parameter has its own cache. This function is therefore slightly less amenable to layout mutations like "changing the options after scaling function is used", but this is not expected to be a common use case.

CAVEAT: Some datasets do not return true datum ids, but instead append synthetic ID fields ("item 1, item2"...) just to appease D3. This hash function only works if there is a meaningful, stable identifier in the data, like a category or gene name.

Parameters:
Name Type Description
parameters
Properties
Name Type Attributes Default Description
values Array <optional>

A list of options to choose from
max_cache_size Number <optional>
 500

The maximum number of values to cache. This option is mostly used for unit testing, because stable choice is intended for datasets with a relatively limited number of discrete categories.
value
index
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(inner) to_rgb(parameters, value)

(extension) Convert a value ""rr,gg,bb" (if given) to a css-friendly color string: "rgb(rr,gg,bb)". This is tailored specifically to the color specification format embraced by the BED file standard.

Parameters:
Name Type Description
parameters Object

This function has no defined configuration options
value String | null

The value to convert to rgb
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