phantasus - Linking

## phantasus Configuration Options

### Please note that the correct HTTP CORS headers must be set if any of your resources are hosted on a different domain.

Load phantasus with a pre-configured matrix

The phantasus website accepts the following request parameters
'json': a URI encoded JSON configuration object.
'url': a URL to a JSON configuration file.
Example
`{columnAnnotations : [ { file : '//s3.amazonaws.com/data.clue.io/morpheus/Achilles_v2.4_SampleInfo_small.txt', datasetField : 'id', fileField : 'id' } ], columns : [ { field : 'id', display : 'text' }, { field : 'Site_primary', display : 'color' } ], dataset : '//s3.amazonaws.com/data.clue.io/morpheus/Achilles_QC_v2.4.3.rnai.Gs.gct'}`
Open Example In phantasus

#### dataset

A File or URL to a GCT 1.3, GCT 1.2, MAF, GMT, or a tab-delimited text file. Can also be an array of File or URLs in which case the datasets are combined by matching on column ids.

#### rowAnnotations/columnAnnotations

Optional array of `{file:String, datasetField:String, fileField:String, include:[String]}`
`file` : An xlsx file, a tab-delimited text file, or a gmt file.
`datasetField` : Field to match in dataset.
`fileField` : Field to match in file.
`include` : Optional array of fields to include from file.
Example: Annotate rows matching 'name' field in dataset to 'id' field in file at https://MY_URL. `[{file:'https://MY_URL', datasetField:'name', fileField:'id'}]`

#### rowGroupBy/columnGroupBy

Optional rray of metadata names to group the heat map by.
Example: Group by the type and gender metadata fields. `['type', 'gender']`

#### colorScheme

Optional object `{type:String, stepped:boolean, map:[{value:Number, color:String}]}` that describes value to color mapping. `type` : 'fixed' or 'relative' color scheme.
`stepped` : Whether color scheme is continuous (false) or discrete (true).
`map` Array of value, color pairs.
Example: Use a fixed color scheme with color stops at -100, -90, 90, and 100.
`{ type : 'fixed', stepped:false, map : [ { value : -100, color : '#abdda4' }, { value : -90, color : 'white' }, { value : 90, color : 'white' }, { value : 100, color : 'red' } ] };`

#### rowSortBy/columnSortBy

Optional array of metadata names and sort order ( `[{field:String, order:Number}]` ).
`field` : Metadata field name.
`order` : 0 for ascending, 1 for descending.
Example: Sort ascending by gene, and then descending by stdev `[{field:'gene', order:0}, {field:'stdev', order:1}]`

#### rowDendrogram/columnDendrogram

Optional URL to a dendrogram in Newick format

#### rowDendrogramField/columnDendrogramField

Optional metadata field in dataset to match leaf node ids in the dendrogram Newick file.

#### rows/columns

Optional array of objects describing how to display metadata fields ( `[{field:String, display:String}]` ).
`field` : Metadata field name
`display` : A comma delimited string that describes how to render a metadata field. Options are text, color, bar, highlight, shape, discrete, and continuous name
Example Display id as text and stdev using text and color `[{field:'id', display:'text'}, {field:'stdev', display:'text, color'}]`

#### tools

Optional array of tools to run at load time `[{name:String, params:Object}]` Example: Cluster rows and columns.
`[{ name: 'Hierarchical Clustering', params: {cluster: 'Rows and columns'} }]`