Deep Linking Into Xena
How to programmatically specify Xena Browser views
Xena has the ability to draw visualizations based on parameters passed through URL. You will need to URL encode the parameters.
The list of supported parameters below is not exhaustive. If you do not see your functionality supported below please contact us.
Display Column Setup Examples
linktest.html
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HTML file showing how to build examples 1 - 7.
Highlight Samples Examples
Example 9: highlight samples matching arbitrary criteria, such as samples in Column B with values > 10
samplehighlight2.html
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HTML files showing how to build examples 8 & 9
Sample Filtering (specify what samples to display in the view) Examples
sample_highlight_filter.html
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HTML file showing how to specify what samples to display in the view
var page = ‘https://xenabrowser.net/heatmap/’;
var url = page + ‘?columns=’ + encodeURIComponent(columns_parameter) + \
‘&heatmap=’ + encodeURIComponent(heatmap_parameter);
The columns parameter is a JSON-encoded array of objects, specifying the columns to display.
To specify a single column you need to, at a minimum, specify the dataset ID, the hub where the data resides, and the fields that you want to display.
var column = {name: dataset1, host: hub1, fields: 'foo bar'};
var columns_parameter = JSON.stringify([column]);
var url = page + ‘?columns=’ + encodeURIComponent(columns_parameter);
Fields can be a gene, probe, or chromosome position. All fields need to be of the same type (i.e. all genes or all probes). You can only enter one chromosome position per column.
Field should be the field ID as it appears exactly in the dataset
width: <number>
Width in pixels
columnLabel: <string>
Text for top column label
fieldLabel: <string>
Text for bottom column label
geneAverage: <boolean>
Display the gene average instead of the individual probes for a gene. You can use this only when a single gene is specified for a dataset that has probes on a gene
normalize: ‘none’ | ‘mean’ | ‘log2’ | ‘normal2’
How the data should be dynamically normalized on the fly. 'mean' is x-mean (subtract mean), applied per (sub)column. 'log2' is log2(x+1). 'normal2' is (x-2).
showIntrons: <boolean>
Show introns for mutation and segmented copy number columns
sortDirection: 'reverse'
Reverse sort the samples
sortVisible: <boolean>
Sort column on the zoomed region
Same as the columns parameter, but these columns will not be displayed. They are available for sample filtering. See the filter property of the heatmap parameter, below.
The heatmap parameter is a JSON-encoded object specifying global display options
mode: 'chart'
Display in chart mode rather than visual spreadsheet mode.
showWelcome: <boolean>
Show the welcome banner.
searchSampleList: [<string>, ...]
Highlight the specified samples in the view.
search: <string>
Equivalent to typing this text into the 'Find' feature in Xena. In this example it is highlighting the samples that for column B have a value of 'TARGET'. More examples of possible search terms.
filter: <string>
Like the search parameter, but filter the view to the matching samples. Equivalent to selecting 'Filter' from the 'Find' UI. Columns that are only needed for filtering (not visualization) can be added to the filterColumns parameter, and appear semantically after columns. For example, if columns has length two they are labeled 'B' and 'C', and the first column in filterColumns will be 'D'.
Both search and filter can be specified in the same url, in which case the samples will be filtered, and any remaining samples matching search will be highlighted. Note that the search expression should only reference columns, not filterColumns, since the latter are not available for visualization.
var heatmap_paramter = JSON.stringify({
showWelcome: false,
search: "B:=TARGET"
});
var url = page + ‘?columns=’ + encodeURIComponent(columns_parameter) + \
‘?heatmap=’ + encodeURIComponent(heatmap_paramter);
Last modified 3yr ago