swh:1:snp:0c004a03453a29b80f921a24433f7e780b9ceb53
Tip revision: 05217c4ed32e001e14eca2b9c32c8a21d363b8b3 authored by Alexey Sergushichev on 11 December 2018, 21:13:22 UTC
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Tip revision: 05217c4
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<h2>phantasus Configuration Options</h2>
<h3>
Please note that the correct HTTP <a target="_blank"
href="https://en.wikipedia.org/wiki/Cross-origin_resource_sharing">CORS</a>
headers must be set if any of your resources are hosted on a
different domain.
</h3>
<p class="text-muted">Load phantasus with a pre-configured matrix</p>
<p>
The phantasus website accepts the following request parameters <br/>'json':
a URI encoded JSON configuration object. <br/>'url': a URL to a
JSON configuration file. <br/> <br/> <b>Example</b><br/>
<code>{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'}</code>
<br/> <a href="#" name="open">Open Example In phantasus</a>
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<h4>
<a data-toggle="collapse">dataset</a>
</h4>
<p class="collapse">
A File or URL to a <a target="_blank"
href="http://support.lincscloud.org/hc/en-us/articles/202105453-GCT-Gene-Cluster-Text-Format-">GCT
1.3</a>, <a target="_blank"
href="http://www.broadinstitute.org/cancer/software/genepattern/gp_guides/file-formats/sections/gct">GCT
1.2</a>, <a target="_blank"
href="https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+%28MAF%29+Specification">MAF</a>,
<a target="_blank"
href="http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29">GMT</a>,
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.
</p>
<h4>
<a data-toggle="collapse">rowAnnotations/columnAnnotations</a>
</h4>
<p class="collapse">
Optional array of
<code>{file:String, datasetField:String, fileField:String,
include:[String]}</code>
<br/>
<code>file</code>
: An xlsx file, a tab-delimited text file, or a gmt file.<br/>
<code>datasetField</code>
: Field to match in dataset.<br/>
<code>fileField</code>
: Field to match in file.<br/>
<code>include</code>
: Optional array of fields to include from file. <br/> <b>Example:</b>
Annotate rows matching 'name' field in dataset to 'id' field in
file at https://MY_URL.
<code>[{file:'https://MY_URL', datasetField:'name',
fileField:'id'}]</code>
</p>
<h4>
<a data-toggle="collapse">rowGroupBy/columnGroupBy</a>
</h4>
<p class="collapse">
Optional rray of metadata names to group the heat map by. <br/> <b>Example:</b>
Group by the type and gender metadata fields.
<code>['type', 'gender']</code>
</p>
<h4>
<a data-toggle="collapse">colorScheme</a>
</h4>
<p class="collapse">
Optional object
<code>{type:String, stepped:boolean, map:[{value:Number,
color:String}]}</code>
that describes value to color mapping.
<code>type</code>
: 'fixed' or 'relative' color scheme.<br/>
<code>stepped</code>
: Whether color scheme is continuous (false) or discrete (true). <br/>
<code>map</code>
Array of value, color pairs.<br/> <b>Example:</b> Use a fixed
color scheme with color stops at -100, -90, 90, and 100. <br/>
<code>{ type : 'fixed', stepped:false, map : [ { value :
-100, color : '#abdda4' }, { value : -90, color : 'white' }, {
value : 90, color : 'white' }, { value : 100, color : 'red' } ] };</code>
</p>
<h4>
<a data-toggle="collapse">rowSortBy/columnSortBy</a>
</h4>
<p class="collapse">
Optional array of metadata names and sort order (
<code>[{field:String, order:Number}]</code>
). <br/>
<code>field</code>
: Metadata field name. <br/>
<code>order</code>
: 0 for ascending, 1 for descending. <br/> <b>Example:</b> Sort
ascending by gene, and then descending by stdev
<code>[{field:'gene', order:0}, {field:'stdev', order:1}]</code>
</p>
<h4>
<a data-toggle="collapse">rowDendrogram/columnDendrogram</a>
</h4>
<p class="collapse">
Optional URL to a dendrogram in <a target="_blank"
href="https://en.wikipedia.org/wiki/Newick_format">Newick
format</a>
</p>
<h4>
<a data-toggle="collapse">rowDendrogramField/columnDendrogramField</a>
</h4>
<p class="collapse">Optional metadata field in dataset to match
leaf node ids in the dendrogram Newick file.</p>
<h4>
<a data-toggle="collapse">rows/columns</a>
</h4>
<p class="collapse">
Optional array of objects describing how to display metadata fields
(
<code>[{field:String, display:String}]</code>
). <br/>
<code>field</code>
: Metadata field name <br/>
<code>display</code>
: A comma delimited string that describes how to render a metadata
field. Options are text, color, bar, highlight, shape, discrete,
and continuous name <br/> <b>Example</b> Display id as text and
stdev using text and color
<code>[{field:'id', display:'text'}, {field:'stdev',
display:'text, color'}]</code>
</p>
<h4>
<a data-toggle="collapse">tools</a>
</h4>
<p class="collapse">
Optional array of tools to run at load time
<code>[{name:String, params:Object}]</code>
<b>Example:</b> Cluster rows and columns. <br/>
<code>[{
name: 'Hierarchical Clustering',
params: {cluster: 'Rows and columns'}
}]</code>
</p>
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function (e) {
var json = {
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'
};
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+ encodeURIComponent(JSON.stringify(json));
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