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
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.
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'}]
Optional rray of metadata names to group the heat map by.
Example:
Group by the type and gender metadata fields.
['type', 'gender']
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' } ] };
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}]
Optional URL to a dendrogram in Newick format
Optional metadata field in dataset to match leaf node ids in the dendrogram Newick file.
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'}]
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'}
}]