Data table settings

This YAML file contains settings for a data table. See also:

Possible keys

nameSingle
Text (required). Display name referring to a single table item (single, without starting capital).
namePlural
Text (required). Display name referring to several table items (plural, without starting capital).
description
Text. Default:. A short description of this data table. This text will appear on the intro page, and on the table view page of this data table. Note: this text may contain documentation links (see Documentation source files).
icon
Text. Specifies an icon that will be associated with the data table. The icon name can be chosen from the list specified in http://fortawesome.github.io/Font-Awesome/icons/.
isHidden
Boolean. If set to true, the data table will not be displayed as a standalone entity (i.e. not mentioned on the intro page and no tab).
primKey
PropertyID (required). The primary key property ID for this table. A data item property is a column in the TAB-delimited source file data, and the ID corresponds to the column header. The primary key should refer to a column containing a unique value for each record in the table. Optionally, this parameter can be set to ‘AutoKey‘ to instruct the software to automatically generate a primary key.
itemTitle
Text. A handlebars template. Defaults to the primary key. The rendered template will be used when a data item title is needed.
sortDefault
PropertyID. Specifies the property ID (i.e. column name in the data source file) used as the default sort field..
defaultQuery
Text. Specifies the default query used thoughout the app for this table..
storedQueries

List. Default:[]. A list of queries to be displayed in the app for this table. The block can contain the following keys:

query
Text (required). a query string.
name
Text (required). a display name for this query.
maxCountQueryRecords
Value. Default:200000. Defines the maximum number of records that will be downloaded to the client. This limit influences views that display individual data items, such as scatter plots and geographical map views. If not specified, this defaults to 200,000.
maxCountQueryAggregated
Value. Default:1000000. Defines the maximum number of records that will be queried on the server for views that present data items in an aggregated way, such as histograms and bar graphs. If not specified, this defaults to 1,000,000.
fetchRecordCount
Boolean. Default:False. .
quickFindFields
PropertyIDs. The list of properties will be used by some tools in the software that allow the user to quickly find a (set of) item(s).
disableSubsets
Boolean. If set, there will be no subsets options for this data table.
disablePlots
Boolean. If set, there will be no options to create plots for this data table.
disableNotes
Boolean. If set, it will not be possible to define notes for items in this data table.
propertyGroups

List. Default:[]. Each item in the list specifies a group of properties. Property groups are used to combine sets of related properties into logical sections in the app. The block can contain the following keys:

id
Text (required). a unique identifier for the group.
name
Text (required). a display name.
properties
List (required). Each list item defines a property, linked to a column in the TAB-delimited source file data. See Datatable property settings settings for an overview of the keys that can be used for each property in this list.
dataItemViews

List. Definitions of custom views that will appear in the popup for an individual data table item. The block can contain the following keys:

type
Text (required). Identifier of the custom view type

(can be Overview, PropertyGroup, FieldList, ItemMap, PieChartMap) See DataItemViews settings for more details about defining custom data item views.

externalLinks

List. Each item in the list specifies a link for a data item to an external url. These links show up in the app as buttons in the data item popup window. The block can contain the following keys:

url
Text (required). Url for this link. This may include tokens property ID’s between curly braces.
These tokens will be expanded to their actual content for a specific data item. Example: http://maps.google.com/maps?q={Latitude},{Longitude}.
name
Text (required). Display name for this external link.
listView
Boolean. Default:False. Replaces the normal table view with a list view, showing rows on left and a single selected row on the right.
isPositionOnGenome
Boolean. Default:False. Instructs Panoptes that records in this data table should be interpreted as genomic positions. In this case, the Chromosome and Position keys should be defined.
isRegionOnGenome
Boolean. Default:False. Instructs Panoptes that records in this datatable should be interpreted as genomic regions. In this case, the Chromosome, RegionStart and RegionStop keys should be defined.
chromosome
PropertyID. Default:chrom. Specifies the table column ID that contains the chromosome (only to be used if IsPositionOnGenome or IsRegionOnGenome is set). Note that the values in this column should correspond to the content of fasta file (see Reference genome source files).
position
PropertyID. Default:pos. Specifies the table column ID that contains the position on the chromosome (only to be used if IsPositionOnGenome is set).
regionStart
PropertyID. Default:start. Specifies the table column ID that contains the start position of the region (only to be used if IsRegionOnGenome is set).
regionStop
PropertyID. Default:stop. Specifies the table column ID that contains the end position of the region (only to be used if IsRegionOnGenome is set).
browserDefaultVisible
Boolean. For genomic regions: specifies the default visibility status of this data table in the genome browser (only to be used if IsRegionOnGenome is set). Note that, for genomic position, default visibility is specified on a per-property basis.
maxTableSize
Value. Default:None. .
browserDefaultLabel
PropertyID. Specifies the default label that is used in the genome browser, used for genomic regions. None indicates that no label is displayed by default.
tableBasedSummaryValues

List. Default:[]. Declares that numerical genome values for are available for each item in the table. Panoptes will process these using the multiresolution filterbanking, and the user can display these as tracks in the genome browser. A typical use case is if the data table contains samples that were sequenced, and there is coverage data available

Approach 1

There should be a subdirectory named after the identifier of this track in the data table source data folder. For each data item, this directory should contain a data file with the name equal to the primary key (see example). The input files should not contain a header row

The Id is the identifier of this set of per-data-item genomic values i.e. the name of the subdirectory

Approach 2

This approach is more like the way the table based data files are processed. In this case multiple tracks can be stored in the same input file. The Id corresponds to the column name instead of the directory name with the directory details given in the FilePattern expression The name is the first match in the FilePattern expression

.
The block can contain the following keys:
id
Text (required). Identifier of this set of per-data-item genomic values - name of subdirectory or Identifier of this set of per-data-item genomic values - name of the column in the matching files.
filePattern
Text. A glob (regular expression) containing a relative path to the file(s).
name
Text (required). Display name of the property.
minVal
Value (required). Default:0. Value used for lower extent of scales.
maxVal
Value (required). Value used for upper extent of scales.
blockSizeMin
Value (required). Default:1. Minimum block size used by the multiresolution summariser (in bp).
blockSizeMax
Value (required). Maximum block size used by the multiresolution summariser (in bp).
channelColor
Text. Colour used to display these tracks as a genome browser track. Formatted as "rgb(r,g,b)".