Configuration v0.0.0

The PanVA application can be configured with a runtime configuration file config.json placed in the root directory of the application. It's recommended to use a config file whenever metadata, annotations, and trees need to be displayed.

Options

All fields are optional.

Field	Type	Default	Description
apiUrl	string	"/api/"	Base URI of the API.
apps	string[]	["homology"]	Apps that should be enabled.
homology	object		Configuration options for the homology app.
homology.alignmentMetadata	Metadata[]	[]	Alignment cell metadata.
homology.annotations	Annotation[]	[]	List of available annotations.
homology.defaultId	integer	The first id in the homologies list.	Default homology group to load.
homology.defaultSequence MetadataColumns	string[]	[]	Default sequence metadata columns to be shown.
homology.homologyMetadata	Metadata[]	[]	Homology group metadata.
homology.sequenceMetadata	Metadata[]	[]	Sequence metadata, user-selectable.
homology.trees	Tree[]	[]	Additional trees.
homology.variableMetadata	Metadata[]	[]	Variable position metadata.
title	string	"PanVA"	Title of the application.

Annotation

Positions can be annotated with one or more features. You can configure which annotations should be displayed.

Each column should be configured as a JSON object with the following options:

Field	Type	Notes
column	string	CSV column in annotations.csv.
label	string	Description of the annotation.

Metadata

Metadata can be visualized in a number of different ways. You can configure which columns should be displayed.

Each column should be configured as a JSON object with the following options:

Field	Type	Notes
column	string	CSV column in the respective file (see note below).
label	string	Name of the column to be displayed.
type	"boolean" | "categorical" | "quantitative"

Based on the value of type these options are extended with the options as defined below.

Important: The same metadata column can not be displayed more than once.

Files

This type is used for several kinds of metadata, which are stored in multiple files:

• alignmentMetadata is stored in alignments.csv and contains metadata for each position in each aligned gene sequence.
• homologyMetadata is stored in homologies.json and contains metadata for each homology group.
• sequenceMetadata is stored in metadata.csv and contains metadata for each aligned gene sequence (metadata is the same for all positions).
• variableMetadata is stored in variable.csv and contains metadata for each variable position (metadata is the same for all sequences).

Metadata of type boolean in variableMetadata can also be used to filter positions.

Type: Boolean

Field	Type	Required	Notes
labels	object		Displayed in tooltip over column.
labels.true	string	✔️
labels.false	string	✔️
labels.null	string	✔️
values	object
values.true	string	✔️	Consider this CSV value to be true.
values.false	string	✔️	Consider this CSV value to be false.

When values is omitted, the value will be matched (case-insensitive) against "true" | "t" | "yes" | "y" for true and "false" | "f" | "no" | "n" for false. All other values will be considered to be unknown (null).

Type: Categorical

Field	Type	Default	Notes
width	number	120	Width of the column for sequence metadata.

Type: Quantitative

Field	Type	Default	Notes
decimals	number	0	Maximum number of decimals to display. Trailing zeroes are removed.
maxValue	number	Maximum value in column	Maximum value to determine bar width.
suffix	string	""	String to be placed behind the numeric value (e.g. "%")
width	number	120	Width of the column for sequence metadata.

Tree

Besides the default and custom dendrogram, PanVA can render additional trees in Newick for. You can configure which columns should be displayed.

Each column should be configured as a JSON object with the following options:

Field	Type	Notes
filename	string	Filename of the tree file (in Newick format) in the root dataset directory.
label	string	Description of the tree.

Example config file

{
  "apiUrl": "/pecto/",
  "homology": {
    "defaultId": "13803671",
    "annotations": [
      {
        "column": "cds",
        "label": "CDS"
      }
    ],
    "sequenceMetadata": [
      {
        "column": "ft16",
        "label": "FT16",
        "type": "quantitative",
        "width": 80
      },
      {
        "column": "virulence",
        "label": "Virulence",
        "labels": {
          "true": "Virulent",
          "false": "Avirulent",
          "null": "Unknown"
        },
        "type": "boolean",
        "values": {
          "true": "virulent",
          "false": "avirulent"
        }
      },
      {
        "column": "species",
        "label": "Species",
        "type": "categorical",
        "width": 80
      },
      {
        "column": "strain_name",
        "label": "Strain",
        "type": "categorical",
        "width": 120
      }
    ],
  },
  "title": "PanVA: Pectobacterium"
}