2D Datatable settings

This YAML file contains settings for a 2D data table. See also:

• Data import settings
• 2D data table source files
• Example file

Possible keys

nameSingle

Text (required). Display name referring to data of an individual cell (single, without starting capital).

namePlural

Text (required). Display name referring to data of several cells (plural, without starting capital).

description

Text. Default:. A short description of this 2D data table. Note: this text may contain documentation links (see Documentation source files).

columnDataTable

Text (required). Identifier of the (1D) data table defining the columns of the matrix (In case of genotype data: the variants). This links the 2D data table to the 1D data table containing the column information.

columnIndexField

Text (required). The property ID in the columnDataTable data table that maps into the columnIndexArray array in the zarr source dir. columnIndexField and columnIndexArray together establish the link between the column data table values, and the data present in the zarr source dir. Alternatively columnIndexArray can be omitted implying that the columns in zarr are in the same order as columnIndexField sorted. Note that “AutoKey” can be used if your rows do not have Unique IDs.

columnIndexArray

Text. 1D Array in the zarr source dir that gives the value of columnIndexField for each column. If this is omitted then it is assumed that the zarr columns are in the same order as the columnDataTable data table, sorted by the columnIndexField property.

rowDataTable

Text (required). Identifier of the (1D) data table defining the rows of the matrix (in case of genotype data: the samples). This links the 2D data table to the 1D data table containing the row information.

rowIndexField

Text (required). The property ID in the rowDataTable data table that maps into rowIndexArray array in the zarr source dir. rowIndexField and rowIndexArray together establish the link between the row data table values, and the data present in the zarr source dir. Alternatively rowIndexArray can be omitted implying that the rows in zarr are in the same order as rowIndexField sorted. Note that “AutoKey” can be used if your rows do not have Unique IDs.

rowIndexArray

Text. 1D Array in the zarr source dir that gives the value of rowIndexField for each row. If this is omitted then it is assumed that the zarr columns are in the same order as the rowDataTable data table, sorted by the rowIndexField property.

showInGenomeBrowser

Block. If this key is present, the data will be visualised as a channel in the genome browser. This requires that data table used as columnDataTable is defined as “IsPositionOnGenome” (see Data table settings) This key contains the following subkeys, Either ‘Call’ or ‘AlleleDepth’ or both must be present. The block can contain the following keys:

call

PropertyID (required). Reference to the 2D data table property that contains call information.

alleleDepth

PropertyID. Reference to the 2D data table property that contains depth information.

extraProperties

PropertyIDList. A list of the extra 2D data table properties that are displayed in the genotype channel. This will populate options for alpha and height control.

properties

List (required). Contains a list of all properties defined for each cell of the 2D data table. The block can contain the following keys:

id

Text (required). Identifier of the property, and name of the dataset in the zarr source dir.

name

Text. Display name of the property.

description

Text. Short description of this property.

minVal

Value. For continuous properties the lower level at which values will be clipped on display.

maxVal

Value. For continuous properties the upper level at which values will be clipped on display.