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.

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Members

(inner) annotation_catalog :panel

A panel that shows a simple annotation track connecting GWAS results

Type:
  • panel
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(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
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(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
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(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
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(inner, constant) annotation_credible_set_tooltip :tooltip

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

Type:
  • tooltip
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(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
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(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
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(inner, constant) association_catalog_panel :panel

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

Type:
  • panel
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(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
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(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
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(inner, constant) association_credible_set_plot :plot

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

Type:
  • plot
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(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
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(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
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(inner) association_pvalues_catalog :data_layer

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

Type:
  • data_layer
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(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
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(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
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(inner) coaccessibility :data_layer

An arc track that shows arcs representing chromatic coaccessibility

Type:
  • data_layer
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(inner) coaccessibility :plot

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

Type:
  • plot
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(inner, constant) coaccessibility_panel :panel

A panel showing chromatin coaccessibility arcs with some common display options

Type:
  • panel
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(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
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(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
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(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
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(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
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(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
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(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:
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(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
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(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
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(inner, constant) intervals_enrichment_panel :panel

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

Type:
  • panel
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(inner, constant) intervals_enrichment_tooltip :tooltip

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

Type:
  • tooltip
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(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
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(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
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(inner, constant) phewas_panel :panel

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

Type:
  • panel
Source:

(inner) phewas_pvalues :data_layer

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

Type:
  • data_layer
Source:

(inner) recomb_rate :data_layer

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

Type:
  • data_layer
Source:

(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:

(inner) significance :data_layer

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

Type:
  • data_layer
Source:

(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
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(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
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(inner, constant) standard_intervals :tooltip

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

Type:
  • tooltip
Source:
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(inner) standard_panel :toolbar

Basic options to remove and reorder panels

Type:
  • toolbar
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(inner) standard_phewas :plot

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

Type:
  • plot
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(inner) standard_plot :toolbar

A simple plot toolbar with buttons to download as image

Type:
  • toolbar
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