# Module: LocusZoom_Layouts

Predefined layouts that describe how to draw common types of data, as well as what interactive features to use. Each plot contains multiple panels (rows), and each row can stack several kinds of data in layers (eg scatter plot and line of significance). Layouts provide the building blocks to provide interactive experiences and user-friendly tooltips for common kinds of genetic data.

Many of these layouts (like the standard association plot) assume that field names are the same as those provided in the UMich portaldev API. Although layouts can be used on many kinds of data, it is often less work to write an adapter that uses the same field names, rather than to modify every single reference to a field anywhere in the layout.

See the Layouts Tutorial for details on how to customize nested layouts.

Source:
  - layouts/index.js, line 1

### Members

#### (inner) annotation_catalog :panel

A panel that shows a simple annotation track connecting GWAS results

##### Type:

- panel

Source:
  - layouts/index.js, line 957

#### (inner, constant) annotation_catalog_layer :data_layer

An annotation / rug track that shows tick marks for each position in which a variant is present in the provided association data, and has a significant claim in the EBI GWAS catalog.

##### Type:

- data_layer

Source:
  - layouts/index.js, line 506

#### (inner, constant) annotation_credible_set :panel

(extension) A panel layout that shows a vertical mark whenever a SNP is a member of the credible set

##### Type:

- panel

Source:
  - ext/lz-credible-sets.js, line 252
See:
  - module:ext/lz-credible-sets for required extension and installation instructions

#### (inner, constant) annotation_credible_set_layer :data_layer

(extension) A data layer layout that shows a vertical mark whenever a SNP is a member of the credible set

##### Type:

- data_layer

Source:
  - ext/lz-credible-sets.js, line 199
See:
  - module:ext/lz-credible-sets for required extension and installation instructions

#### (inner, constant) annotation_credible_set_tooltip :tooltip

(extension) A tooltip layout for annotation (rug) tracks that provides information about credible set members

##### Type:

- tooltip

Source:
  - ext/lz-credible-sets.js, line 144
See:
  - module:ext/lz-credible-sets for required extension and installation instructions

#### (inner) association :panel

A panel that describes the most common kind of LocusZoom plot, with line of GWAS significance, recombination rate, and a scatter plot superimposed.

##### Type:

- panel

Source:
  - layouts/index.js, line 735

#### (inner) association_catalog :plot

A modified version of the standard LocusZoom plot, which adds a track that shows which SNPs in the plot also have claims in the EBI GWAS catalog.

##### Type:

- plot

Source:
  - layouts/index.js, line 1005

#### (inner, constant) association_catalog_panel :panel

A panel showing GWAS summary statistics, plus annotations for connecting it to the EBI GWAS catalog

##### Type:

- panel

Source:
  - layouts/index.js, line 833

#### (inner, constant) association_credible_set :panel

(extension) A panel layout that shows GWAS summary statistics in a standard LocusZoom view, overlaid with credible set membership information

##### Type:

- panel

Source:
  - ext/lz-credible-sets.js, line 280
See:
  - module:ext/lz-credible-sets for required extension and installation instructions

#### (inner, constant) association_credible_set_layer :data_layer

(extension) A data layer layout that shows GWAS summary statistics overlaid with credible set membership information

##### Type:

- data_layer

Source:
  - ext/lz-credible-sets.js, line 161
See:
  - module:ext/lz-credible-sets for required extension and installation instructions

#### (inner, constant) association_credible_set_plot :plot

(extension) A standard LocusZoom plot layout, with additional credible set information.

##### Type:

- plot

Source:
  - ext/lz-credible-sets.js, line 397
See:
  - module:ext/lz-credible-sets for required extension and installation instructions

#### (inner, constant) association_credible_set_tooltip :tooltip

(extension) Tooltip layout that appends credible set posterior probability to the default association tooltip (for SNPs in the credible set)

##### Type:

- tooltip

Source:
  - ext/lz-credible-sets.js, line 129
See:
  - module:ext/lz-credible-sets for required extension and installation instructions

#### (inner) association_pvalues :data_layer

A scatter plot of GWAS association summary statistics, with preset field names matching the UM portaldev api

##### Type:

- data_layer

Source:
  - layouts/index.js, line 138

#### (inner) association_pvalues_catalog :data_layer

A scatter plot of GWAS summary statistics, with additional tooltip fields showing GWAS catalog annotations

##### Type:

- data_layer

Source:
  - layouts/index.js, line 319

#### (inner, constant) bed_intervals :panel

(extension) A panel containing an intervals data layer, eg for BED tracks. These field names match those returned by the LzParsers extension.

##### Type:

- panel

Source:
  - ext/lz-intervals-track.js, line 755
See:
  - module:ext/lz-intervals-track for required extension and installation instructions

#### (inner, constant) bed_intervals_layer :data_layer

(extension) A data layer with some preconfigured options for intervals display. This example was designed for standard BED3+ files and the field names emitted by the LzParsers extension.

##### Type:

- data_layer

Source:
  - ext/lz-intervals-track.js, line 678
See:
  - module:ext/lz-intervals-track for required extension and installation instructions

#### (inner) coaccessibility :data_layer

An arc track that shows arcs representing chromatic coaccessibility

##### Type:

- data_layer

Source:
  - layouts/index.js, line 252

#### (inner) coaccessibility :plot

Show chromatin coaccessibility arcs, with additional features that connect these arcs to nearby genes to show regulatory interactions.

##### Type:

- plot

Source:
  - layouts/index.js, line 1051

#### (inner, constant) coaccessibility_panel :panel

A panel showing chromatin coaccessibility arcs with some common display options

##### Type:

- panel

Source:
  - layouts/index.js, line 796

#### (inner, constant) gene_selector_menu :toolbar_widgets

A dropdown menu that selects which types of genes to show in the plot. The provided options are curated sets of interesting gene types based on the GENCODE dataset.

##### Type:

- toolbar_widgets

Source:
  - layouts/index.js, line 587

#### (inner) genes_filtered :data_layer

A genes data layer that uses filters to limit what information is shown by default. This layer hides a curated list of GENCODE gene_types that are of less interest to most analysts. Often used in tandem with a panel-level toolbar "show all" button so that the user can toggle to a full view.

##### Type:

- data_layer

Source:
  - layouts/index.js, line 474

#### (inner, constant) genes_layer :data_layer

Shows genes in the specified region, with names and formats drawn from the UM Portaldev API and GENCODE datasource

##### Type:

- data_layer

Source:
  - layouts/index.js, line 443

#### (inner, constant) genes_panel :panel

A panel showing genes in the specified region. This panel lets the user choose which genes are shown.

##### Type:

- panel

Source:
  - layouts/index.js, line 894

#### (inner, constant) interval_association :plot

(extension) A plot layout that shows association summary statistics, genes, and interval data. This example assumes chromHMM data. (see panel layout) Few people will use the full intervals plot layout directly outside of an example.

##### Type:

- plot

Source:
  - ext/lz-intervals-track.js, line 769
See:
  - module:ext/lz-intervals-track for required extension and installation instructions

#### (inner, constant) intervals :panel

(extension) A panel containing an intervals data layer, eg for BED tracks. This is a legacy layout whose field names were specific to one partner site.

##### Type:

- panel

Source:
  - ext/lz-intervals-track.js, line 719
See:
  - module:ext/lz-intervals-track for required extension and installation instructions

#### (inner, constant) intervals_association_enrichment :plot

(extension) A plot layout that shows association summary statistics, genes, and intervals-by-enrichment data. This layout provides interactive matching: clicking an interval marking causes area of the scatter plot to be highlighted for any annotations that match the specified category. It is intended to work with data in the HuGeAMP format.

##### Type:

- plot

Source:
  - ext/lz-intervals-enrichment.js, line 293
See:
  - module:ext/lz-intervals-enrichment for required extension and installation instructions

#### (inner, constant) intervals_enrichment_data_layer :data_layer

(extension) A data layer with some preconfigured options for intervals-by-enrichment display, in which intervals are ranked by priority from enrichment analysis.

##### Type:

- data_layer

Source:
  - ext/lz-intervals-enrichment.js, line 174
See:
  - module:ext/lz-intervals-enrichment for required extension and installation instructions

#### (inner, constant) intervals_enrichment_panel :panel

(extension) A panel containing an intervals-by-enrichment data layer

##### Type:

- panel

Source:
  - ext/lz-intervals-enrichment.js, line 255
See:
  - module:ext/lz-intervals-enrichment for required extension and installation instructions

#### (inner, constant) intervals_enrichment_tooltip :tooltip

(extension) A basic tooltip with information to be shown over an intervals-by-enrichment datum

##### Type:

- tooltip

Source:
  - ext/lz-intervals-enrichment.js, line 155
See:
  - module:ext/lz-intervals-enrichment for required extension and installation instructions

#### (inner, constant) intervals_layer :data_layer

(extension) A data layer with some preconfigured options for intervals display. This example was designed for chromHMM output, in which various states are assigned numeric state IDs and (<= as many) text state names.

This layout is deprecated; most usages would be better served by the bed_intervals_layer layout instead.

##### Type:

- data_layer

Source:
  - ext/lz-intervals-track.js, line 623
See:
  - module:ext/lz-intervals-track for required extension and installation instructions

#### (inner) ldlz2_pop_selector :toolbar_widgets

A dropdown menu that can be used to control the LD population used with the LDServer Adapter. Population names are provided for the 1000G dataset that is used by the offical UM LD Server.

##### Type:

- toolbar_widgets

Source:
  - layouts/index.js, line 552

#### (inner, constant) phewas_panel :panel

A panel that displays PheWAS scatter plots and automatically generates a color scheme

##### Type:

- panel

Source:
  - layouts/index.js, line 927

#### (inner) phewas_pvalues :data_layer

A scatter plot of PheWAS pvalues, with preset field names matching the UM Portaldev API

##### Type:

- data_layer

Source:
  - layouts/index.js, line 342

#### (inner) recomb_rate :data_layer

A simple curve representing the genetic recombination rate, drawn from the UM API

##### Type:

- data_layer

Source:
  - layouts/index.js, line 109

#### (inner) region_nav_plot :toolbar

A basic plot toolbar with buttons to scroll sideways or zoom in. Useful for all region-based plots.

##### Type:

- toolbar

Source:
  - layouts/index.js, line 678

#### (inner) significance :data_layer

A horizontal line of GWAS significance at the standard threshold of p=5e-8

##### Type:

- data_layer

Source:
  - layouts/index.js, line 96

#### (inner) standard_association :plot

Describes how to fetch and draw each part of the most common LocusZoom plot (with field names that reference the portaldev API)

##### Type:

- plot

Source:
  - layouts/index.js, line 987

#### (inner, constant) standard_association_toolbar :toolbar

A plot toolbar that adds a button for controlling LD population. This is useful for plots intended to show GWAS summary stats, which is one of the most common usages of LocusZoom.

##### Type:

- toolbar

Source:
  - layouts/index.js, line 671

#### (inner, constant) standard_intervals :tooltip

(extension) A basic tooltip with information to be shown over an intervals datum

##### Type:

- tooltip

Source:
  - ext/lz-intervals-track.js, line 607
See:
  - module:ext/lz-intervals-track for required extension and installation instructions

#### (inner) standard_panel :toolbar

Basic options to remove and reorder panels

##### Type:

- toolbar

Source:
  - layouts/index.js, line 612

#### (inner) standard_phewas :plot

A PheWAS scatter plot with an additional track showing nearby genes, to put the region in biological context.

##### Type:

- plot

Source:
  - layouts/index.js, line 1024

#### (inner) standard_plot :toolbar

A simple plot toolbar with buttons to download as image

##### Type:

- toolbar

Source:
  - layouts/index.js, line 639