2D Datatable settings

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

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 HDF5 source file. columnIndexField and columnIndexArray together establish the link between the column data table values, and the data present in the HDF5 source file. Alternatively columnIndexArray can be omitted implying that the columns in HDF5 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 HDF5 source file that gives the value of columnIndexField for each column. If this is omitted then it is assumed that the HDF5 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 HDF5 source file. rowIndexField and rowIndexArray together establish the link between the row data table values, and the data present in the HDF5 source file. Alternatively rowIndexArray can be omitted implying that the rows in HDF5 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 HDF5 source file that gives the value of rowIndexField for each row. If this is omitted then it is assumed that the HDF5 columns are in the same order as the rowDataTable data table, sorted by the rowIndexField property.
symlinkData
Boolean. Default:False. If true then the HDF5 source file will not be copied but only symlinked. Note that if your HDF5 doesn’t have small enough chunking (max few MB per chunk) then performance will suffer. The default of False copies and rechunks the HDF5.
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 HDF5 source file.
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.