JSDoc: Namespace: plot

Sub-module grouping plotting methods.

Properties:

Name	Type	Description
`manhattan`	function	`plco.plot.manhattan`
`manhattan2`	function	`plco.plot.manhattan2`
`qq`	function	`plco.plot.qq`
`qq2`	function	`plco.plot.qq2`
`pca`	function	`plco.plot.pca`
`pca2`	function	`plco.plot.pca2`
`barchart`	function	`plco.plot.barchart`

Source:

plco.js, line 874

Members

(static) helpers

A collection of helper methods for plotting, not intended to be used on its own.

Source:

plco.js, line 2196

Methods

(static) barchart(div_id, phenotype_id, to_jsonopt, customLayoutopt, customConfigopt)

Generates a Plotly barchart showing the breakdown of participants by gender and ancestry for that phenotype.

Parameters:

Name	Type	Attributes	Default	Description
`div_id`	string			The id of the div element, if it does not exist, a new div will be created.
`phenotype_id`	number			A phenotype id.
`to_json`	boolean	<optional>	false	Optional. If true, returns a stringified JSON object containing traces and layout. Else, returns a div element containing the Plotly graph.
`customLayout`	object	<optional>	{}	Optional. Contains Plotly supported layout key-values pair that will overwrite the default layout. Commonly overwritten values may include height and width of the graph. See: https://plotly.com/javascript/reference/layout/ for more details. Also, set `to_json` to true to see what the default layout is.
`customConfig`	object	<optional>	{}	Optional. Contains Plotly supported config key-values pair that will overwrite the default config. See: https://github.com/plotly/plotly.js/blob/master/src/plot_api/plot_config.js#L22-L86 for full details.

Source:

plco.js, line 2064

Returns:

A div element or a string if to_json is true.

(static) manhattan(div_id, phenotype_idopt, sexopt, ancestryopt, p_value_nlog_minopt, chromosomeopt, to_jsonopt, customLayoutopt, customConfigopt)

Generates a Plotly manhattan plot at the given div element with support for a single input.

Parameters:

Name	Type	Attributes	Default	Description
`div_id`	string			The id of the div element. If it does not exist, a new div will be created.
`phenotype_id`	number	<optional>	3080	A phenotype id.
`sex`	string	<optional>	female	A sex, which may be "all, "female", or "male".
`ancestry`	string	<optional>	european	An ancestry, which may be "african_american", "east_asian" or "european".
`p_value_nlog_min`	number	<optional>	2	A numeric value >= 0 specifying the minimum -log10(p) for variants.
`chromosome`	integer	<optional>		Optional A single chromosome. If no chromosome argument is passed, then assume all chromosomes.
`to_json`	boolean	<optional>	false	Optional If true, returns a stringified JSON object containing traces and layout. If false, returns a div element containing the Plotly graph.
`customLayout`	object	<optional>	{}	Optional. Contains Plotly supported layout key-values pair that will overwrite the default layout. Commonly overwritten values may include height and width of the graph. See: https://plotly.com/javascript/reference/layout/ for more details. Also, set `to_json` to true to see what the default layout is.
`customConfig`	object	<optional>	{}	Optional. Contains Plotly supported config key-values pair that will overwrite the default config. See: https://github.com/plotly/plotly.js/blob/master/src/plot_api/plot_config.js#L22-L86 for full details.

Source:

plco.js, line 907

Returns:

A div element or a string if 'to_json' is true.

Example

plco.plot.manhattan()
plco.plot.manhattan('plot', 3080, "female", "european", 2, 18)

(static) manhattan2(div_id, arrayOfObjects, p_value_nlog_minopt, chromosomeopt, to_jsonopt, customLayoutopt, customConfigopt)

Generates a Plotly manhattan plot at the given div element with support for multiple inputs.

Parameters:

Name	Type	Attributes	Default	Description
`div_id`	string			The id of the div element. If it does not exist, a new div will be created.
`arrayOfObjects`	Array			Accepts an array of objects containing the following keys: phenotype_id, sex, ancestry.
`p_value_nlog_min`	number	<optional>	2	A numeric value >= 0 specifying the minimum -log10(p) for variants.
`chromosome`	number	<optional>		Optional. Leave it undefined to plot all chromosomes. Else use an integer [1-22].
`to_json`	boolean	<optional>	false	Optional If true, returns a stringified JSON object containing traces and layout. If false, returns a div element containing the Plotly graph.
`customLayout`	object	<optional>	{}	Optional. Contains Plotly supported layout key-values pair that will overwrite the default layout. Commonly overwritten values may include height and width of the graph. See: https://plotly.com/javascript/reference/layout/ for more details. Also, set `to_json` to true to see what the default layout is.
`customConfig`	object	<optional>	{}	Optional. Contains Plotly supported config key-values pair that will overwrite the default config. See: https://github.com/plotly/plotly.js/blob/master/src/plot_api/plot_config.js#L22-L86 for full details.

Source:

plco.js, line 1162

Returns:

A div element or a string if 'to_json' is true.

Example

await plco.plot.manhattan2('plot', [{phenotype_id: 3080, ancestry: 'european', sex: 'female'},{phenotype_id: 3080, ancestry: 'east_asian', sex: 'female'}])

(static) pca(div_id, phenotype_id, sex, ancestry, to_jsonopt, customLayoutopt, customConfigopt)

Generates a Plotly PCA plot at the given div element with support for a single input.

Parameters:

Name	Type	Attributes	Default	Description
`div_id`	string			The id of the div element, if it does not exist, a new div will be created.
`phenotype_id`	number			A phenotype id.
`sex`	string			A sex, which may be "all", "female", or "male".
`ancestry`	string			A character vector specifying ancestries to retrieve data for.
`to_json`	boolean	<optional>	false	Optional. If true, returns a stringified JSON object containing traces and layout. Else, returns a div element containing the Plotly graph.
`customLayout`	object	<optional>	{}	Optional. Contains Plotly supported layout key-values pair that will overwrite the default layout. Commonly overwritten values may include height and width of the graph. See: https://plotly.com/javascript/reference/layout/ for more details. Also, set `to_json` to true to see what the default layout is.
`customConfig`	object	<optional>	{}	Optional. Contains Plotly supported config key-values pair that will overwrite the default config. See: https://github.com/plotly/plotly.js/blob/master/src/plot_api/plot_config.js#L22-L86 for full details.

Source:

plco.js, line 1883

Returns:

A div element or a string if to_json is true.

Example

await plco.plot.pca('plot', 3080, 'female', 'east_asian')

(static) pca2(div_id, arrayOfObjects, to_jsonopt, customLayoutopt, customConfigopt)

Generates a Plotly PCA plot at the given div element with support for multiple inputs.

Parameters:

Name	Type	Attributes	Default	Description
`div_id`	string			The id of the div element, if it does not exist, a new div will be created.
`arrayOfObjects`	Array			Accepts an array of objects containing the following keys: phenotype_id, sex, ancestry.
`to_json`	boolean	<optional>	false	Optional. If true, returns a stringified JSON object containing traces and layout. Else, returns a div element containing the Plotly graph.
`customLayout`	object	<optional>	{}	Optional. Contains Plotly supported layout key-values pair that will overwrite the default layout. Commonly overwritten values may include height and width of the graph. See: https://plotly.com/javascript/reference/layout/ for more details. Also, set `to_json` to true to see what the default layout is.
`customConfig`	object	<optional>	{}	Optional. Contains Plotly supported config key-values pair that will overwrite the default config. See: https://github.com/plotly/plotly.js/blob/master/src/plot_api/plot_config.js#L22-L86 for full details.

Source:

plco.js, line 1907

Returns:

A div element or a string if to_json is true.

Example

await plco.plot.pca2('plot', [{phenotype_id: 3080, sex: 'female', ancestry: 'east_asian'}, {phenotype_id: 3080, sex: 'female', ancestry: 'european'}])

(static) qq(div_id, phenotype_idopt, sexopt, ancestryopt, to_jsonopt, customLayoutopt, customConfigopt)

Generates a Plotly quartile-quartile plot at the given div element with support for a single input.

Parameters:

Name	Type	Attributes	Default	Description
`div_id`	string			The id of the div element, if it does not exist, a new div will be created.
`phenotype_id`	number	<optional>	3080	A phenotype id.
`sex`	string	<optional>	female	A sex, which may be "all", "female", or "male".
`ancestry`	string	<optional>	east_asian	A character vector specifying ancestries to retrieve data for.
`to_json`	boolean	<optional>	false	Optional. If true, returns a stringified JSON object containing traces and layout. Else, returns a div element containing the Plotly graph.
`customLayout`	object	<optional>	{}	Optional. Contains Plotly supported layout key-values pair that will overwrite the default layout. Commonly overwritten values may include height and width of the graph. See: https://plotly.com/javascript/reference/layout/ for more details. Also, set `to_json` to true to see what the default layout is.
`customConfig`	object	<optional>	{}	Optional. Contains Plotly supported config key-values pair that will overwrite the default config. See: https://github.com/plotly/plotly.js/blob/master/src/plot_api/plot_config.js#L22-L86 for full details.

Source:

plco.js, line 1486

Returns:

A div element or a string if to_json is true.

Example

await plco.plot.qq('plot', 3080, 'female', 'east_asian')

(static) qq2(div_id, arrayOfObjects, to_jsonopt, customLayoutopt, customConfigopt)

Generates a Plotly quartile-quartile plot at the given div element with support for multiple inputs.

Parameters:

Name	Type	Attributes	Default	Description
`div_id`	string			The id of the div element, if it does not exist, a new div will be created.
`arrayOfObjects`	Array			Accepts an array of objects containing the following keys: phenotype_id, sex, ancestry.
`to_json`	boolean	<optional>	false	Optional. If true, returns a stringified JSON object containing traces and layout. Else, returns a div element containing the Plotly graph.
`customLayout`	object	<optional>	{}	Optional. Contains Plotly supported layout key-values pair that will overwrite the default layout. Commonly overwritten values may include height and width of the graph. See: https://plotly.com/javascript/reference/layout/ for more details. Also, set `to_json` to true to see what the default layout is.
`customConfig`	object	<optional>	{}	Optional. Contains Plotly supported config key-values pair that will overwrite the default config. See: https://github.com/plotly/plotly.js/blob/master/src/plot_api/plot_config.js#L22-L86 for full details.

Source:

plco.js, line 1724

Returns:

A div element or a string if to_json is true.

Example

await plco.plot.qq2('plot', [{phenotype_id:3080, sex:'female', ancestry:'east_asian'}, {phenotype_id:3080, sex:'female', ancestry:'european'}, {phenotype_id: 3550, sex:'all', ancestry:'east_asian'}])