### Execute start script

Source: https://ucsc-xena.gitbook.io/project/local-xena-hub/hubs-for-institutions-collaborations-labs-and-larger-projects.md

Runs the configured start script to launch the hub.

```bash
./start_script
```

--------------------------------

### Install xenaPython

Source: https://ucsc-xena.gitbook.io/project/overview-of-features/accessing-data-through-python.md

Commands to install or upgrade the xenaPython library from the GitHub repository.

```bash
pip install 'git+https://github.com/ucscXena/xenaPython'
pip install --upgrade 'git+https://github.com/ucscXena/xenaPython'
```

--------------------------------

### Query documentation via HTTP GET

Source: https://ucsc-xena.gitbook.io/project/llms.txt

Perform a GET request to the documentation index with specific question and goal parameters.

```http
GET https://ucsc-xena.gitbook.io/project/master.md?ask=<question>&goal=<end_goal>
```

--------------------------------

### Create Xena Hub start script

Source: https://ucsc-xena.gitbook.io/project/local-xena-hub/hubs-for-institutions-collaborations-labs-and-larger-projects.md

Defines environment variables and executes the Xena server jar in the background.

```bash
#!/bin/bash

PORT=7222
LOGFILE=xena/xena7222.log 
DOCROOT=xena/files
DB=xena/myHub

java -jar server.jar -r ${DOCROOT} -d ${DB} --no-gui -p ${PORT} -H 0.0.0.0 --logfile ${LOGFILE} --certfile ${CERTFILE} --keyfile ${KEYFILE}> log 2>&1 &

disown
```

--------------------------------

### Probemap File Format

Source: https://ucsc-xena.gitbook.io/project/local-xena-hub/loading-data-from-the-command-line.md

Example of a tab-delimited probemap file structure.

```text
#id    gene    chrom    chromStart    chromEnd    strand 
id_1    AADACL3    chr1    12776118    12776347    +
```

--------------------------------

### Retrieve Dataset Samples and Probe Values

Source: https://ucsc-xena.gitbook.io/project/overview-of-features/accessing-data-through-python.md

Example demonstrating how to fetch samples from a dataset and retrieve specific probe values using the xenaPython API.

```python
import xenaPython as xena

hub = "https://toil.xenahubs.net"
dataset = "tcga_RSEM_gene_tpm"
samples = xena.dataset_samples (hub, dataset, None)
samples = xena.dataset_samples (hub, dataset, 10)
samples = ["TCGA-02-0047-01","TCGA-02-0055-01","TCGA-02-2483-01"]
probes = ['ENSG00000282740.1', 'ENSG00000000005.5']
[position, [ENSG00000282740_1, ENSG00000000005_5]] = xena.dataset_probe_values (hub, dataset, samples, probes)
ENSG00000282740_1
[-9.9658, -2.8262, -9.9658]
```

--------------------------------

### Data File Metadata with Probemap Reference

Source: https://ucsc-xena.gitbook.io/project/local-xena-hub/loading-data-from-the-command-line.md

Example metadata file referencing a specific probemap.

```json
{"type":"genomicMatrix", 
 "cohort":"TCGA Breast Cancer", 
 ":probeMap":"/unc_v2_exon_hg19_probe_TCGA"}
```

--------------------------------

### Set script permissions

Source: https://ucsc-xena.gitbook.io/project/local-xena-hub/hubs-for-institutions-collaborations-labs-and-larger-projects.md

Grants execute permissions to the start script.

```bash
chmod u+x start_script
```

--------------------------------

### Generating Dynamic Xena Links

Source: https://ucsc-xena.gitbook.io/project/technical-documentation/deep-linking-into-xena.md

A complete HTML/JavaScript example showing how to programmatically set href attributes for multiple links with different sample highlighting and filtering configurations.

```html
<html>
<script>
	window.onload = function() {
		var browser = 'http://dev.xenabrowser.net/';
		var columns = JSON.stringify([
			{
				"width": 90,
				"columnLabel": "",
				"fieldLabel": "site id",
				"host": "https://xena.treehouse.gi.ucsc.edu",
				"name": "clinical_TumorCompendium_v11_PolyA_2020-04-09.tsv",
				"fields": "site_id"
			},
			{
				"width": 150,
				"columnLabel": "gene expression RNAseq",
				"fieldLabel": "ALK",
				"host": "https://xena.treehouse.gi.ucsc.edu",
				"name": "TumorCompendium_v11_PolyA_AllSamples_AllGenes_Kallisto_HugoLog2TPM_20230630.tsv",
				"fields": "ALK"
			}
		]);


		var heatmap1 = JSON.stringify({
			showWelcome: false,
			searchSampleList: ["THR30_0820_S01", "THR30_0861_S01"]
		});

		var l1 = document.getElementById('link1');
		l1.href = browser + 'heatmap/?columns=' + encodeURIComponent(columns) + '&heatmap=' + encodeURIComponent(heatmap1);

		var heatmap2 = JSON.stringify({
			showWelcome: false,
			search: "B:=TARGET"
		});

		var l2 = document.getElementById('link2');
		l2.href = browser + 'heatmap/?columns=' + encodeURIComponent(columns) + '&heatmap=' + encodeURIComponent(heatmap2);

		var heatmap3 = JSON.stringify({
			filter: "B:TARGET",
		});

		l3.href = browser + 'heatmap/?columns=' + encodeURIComponent(columns) + '&heatmap=' + encodeURIComponent(heatmap3);

		var heatmap4 = JSON.stringify({
			showWelcome: false,
			filter: "B:TARGET OR B:TCGA",
		});

		l4.href = browser + 'heatmap/?columns=' + encodeURIComponent(columns) + '&heatmap=' + encodeURIComponent(heatmap4);

		var heatmap5 = JSON.stringify({
			showWelcome: false,
			filter: "B: TARGET",
			searchSampleList: ["TARGET-40-0A4I6O-01A-01R"]
		});

		l5.href = browser + 'heatmap/?columns=' + encodeURIComponent(columns) + '&heatmap=' + encodeURIComponent(heatmap5);

		var filterColumns = JSON.stringify([{
			"host": "https://xena.treehouse.gi.ucsc.edu",
			"name": "clinical_TumorCompendium_v11_PolyA_2020-04-09.tsv",
			"fields": "age_at_dx"
		}]);
		var heatmap6 = JSON.stringify({
			showWelcome: false,
			filter: "D:<5",
		});
		var l6 = document.getElementById('link6');
		l6.href = browser + 'heatmap/?columns=' + encodeURIComponent(columns) + '&filterColumns=' + encodeURIComponent(filterColumns) + '&heatmap=' + encodeURIComponent(heatmap6);
	};
</script>
<body>
	<a id=link1>Sample highlight Example 1:</a> highlight samples of specific sample IDs, such as THR30_0820_S01 or THR30_0861_S01
	<br><br>
	<a id=link2>Sample highlight Example 2:</a> highlight samples matching an arbitary criteria, such as TARGET samples
	<br><br>
	<a id=link3>Sample filtering Example 1:</a> specify (filter to) what samples to show in a view using a predicate, such as TARGET samples
	<br><br>
	<a id=link4>Sample filtering Example 2:</a> specify samples in a view using a predicate that includes a boolean term, such as TARGET and TCGA samples (use boolean OR)
	<br><br>
	<a id=link5>Sample filtering and highlight at the same time:</a> specify samples in a view using a predicate (e.g. just show TARGET samples), as well as highlight specific samples by IDs, such as TARGET-40-0A4I6O-01A-01R
	<br><br>
	<a id=link6>Sample filtering using data in a hidden filter column:</a> useful when you want to filter samples using data not displayed on the screen. You can use <i>HIDDEN FILTER COLUMN</i>. For exmaple, filter the samples to < 5 years old, but you don't want to actually display the age column on the screen.  
</body>
</html>
```

--------------------------------

### GET /project/master.md

Source: https://ucsc-xena.gitbook.io/project/llms.txt

Performs a natural language query against the documentation index to retrieve an answer and relevant sources.

```APIDOC
## GET /project/master.md

### Description
Perform an HTTP GET request on the documentation index with the `ask` parameter, and the optional `goal` parameter to retrieve a direct answer and relevant excerpts from the documentation.

### Method
GET

### Endpoint
https://ucsc-xena.gitbook.io/project/master.md

### Parameters
#### Query Parameters
- **ask** (string) - Required - The immediate question to ask, written in natural language.
- **goal** (string) - Optional - Describes the broader end goal to help tailor the answer.
```

--------------------------------

### GET /heatmap/

Source: https://ucsc-xena.gitbook.io/project/technical-documentation/deep-linking-into-xena.md

Constructs a URL to open the UCSC Xena heatmap browser with specific data columns and heatmap configuration parameters.

```APIDOC
## GET /heatmap/

### Description
Opens the UCSC Xena heatmap browser with a pre-defined set of columns and heatmap settings such as sample highlights or filters.

### Endpoint
https://xenabrowser.net/heatmap/

### Query Parameters
- **columns** (string) - Required - A JSON-encoded array of column objects defining the data sources (host, name, fields) to display.
- **heatmap** (string) - Optional - A JSON-encoded object defining heatmap settings like `showWelcome`, `searchSampleList`, `search`, or `filter`.
- **filterColumns** (string) - Optional - A JSON-encoded array of column objects used for hidden filtering criteria.

### Request Example
https://xenabrowser.net/heatmap/?columns=%5B%7B%22host%22%3A%22https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%22%2C%22name%22%3A%22clinical_TumorCompendium_v11_PolyA_2020-04-09.tsv%22%2C%22fields%22%3A%22site_id%22%7D%5D&heatmap=%7B%22searchSampleList%22%3A%5B%22THR30_0820_S01%22%5D%7D
```

--------------------------------

### Configure colNormalization in genomicMatrix metadata

Source: https://ucsc-xena.gitbook.io/project/technical-documentation/metadata-specification-1.md

Example configuration object for a genomicMatrix dataset using the colNormalization parameter.

```javascript
{
     "cohort": "TCGA Acute Myeloid Leukemia (LAML)",
     "dataSubType": "gene expression RNAseq",
     "label": "IlluminaHiSeq",
     "colNormalization": true,
     "type": "genomicMatrix",
     "unit": "log2(norm_count+1)"
}
```

--------------------------------

### Delete data via command line

Source: https://ucsc-xena.gitbook.io/project/local-xena-hub/hubs-for-institutions-collaborations-labs-and-larger-projects.md

Remove data files from the hub using the -x option. Note that the example for a custom port uses the -l flag in the source text.

```bash
java -jar server.jar -x /path/to/root/file.tsv
```

```bash
java -jar server.jar -p ${PORT} -l /path/to/root/file.tsv
```

--------------------------------

### Display Help Information

Source: https://ucsc-xena.gitbook.io/project/local-xena-hub/loading-data-from-the-command-line.md

Access the command-line help menu to view available options.

```bash
java -jar cavm-0.xx.0-standalone.jar -h
```

--------------------------------

### Deep Linking with Sample Highlighting and Filtering

Source: https://ucsc-xena.gitbook.io/project/technical-documentation/deep-linking-into-xena.md

Demonstrates how to construct dynamic URLs for the Xena browser using JavaScript to encode column configurations and heatmap parameters for sample highlighting and filtering.

```html
<html>
<script>
	window.onload = function() {
		var browser = 'https://xenabrowser.net/';
		var columns = JSON.stringify([
			{
				"width": 136,
				"columnLabel": "gene expression RNAseq - IlluminaHiSeq",
				"fieldLabel": "TP53",
				"showIntrons": true,
				"host": "https://tcga.xenahubs.net",
				"name": "TCGA.BRCA.sampleMap/HiSeqV2",
				"fields": "TP53"
			},
			{
				"width": 200,
				"columnLabel": "somatic mutation (SNPs and small INDELs) - MC3 public version",
				"fieldLabel": "TP53",
				"host": "https://tcga.xenahubs.net",
				"name": "mc3/BRCA_mc3.txt",
				"fields": "TP53"
			}
		]);


		var heatmap1 = JSON.stringify({
			showWelcome: false,
			searchSampleList: ["TCGA-C8-A131-01", "TCGA-BH-A0DL-01"]
		});

		var l1 = document.getElementById('link1');
		l1.href = browser + 'heatmap/?columns=' + encodeURIComponent(columns) + '&heatmap=' + encodeURIComponent(heatmap1);

		var heatmap2 = JSON.stringify({
			showWelcome: false,
			search: "B:>10"
		});

		var l2 = document.getElementById('link2');
		l2.href = browser + 'heatmap/?columns=' + encodeURIComponent(columns) + '&heatmap=' + encodeURIComponent(heatmap2);
	};
</script>
<body>
	<a id=link1>Sample highlight example 1:</a> highlight samples of specific sample IDs, such as TCGA-C8-A131-01 or TCGA-BH-A0DL-01
	<br>
	<a id=link2>Sample highlight example 2:</a> highlight samples matching arbitary criteria, such as samples in Column B with values > 10
</body>
</html>
```

--------------------------------

### Configure Xena Hub database path

Source: https://ucsc-xena.gitbook.io/project/local-xena-hub/hubs-for-institutions-collaborations-labs-and-larger-projects.md

Sets the location for the database file, defaulting to ${HOME}/xena/database.

```bash
--database -d default to ${HOME}/xena/database
```

--------------------------------

### Configure Xena Hub log file path

Source: https://ucsc-xena.gitbook.io/project/local-xena-hub/hubs-for-institutions-collaborations-labs-and-larger-projects.md

Sets the location for the log file, defaulting to ${HOME}/xena/xena.log.

```bash
--logfile default to ${HOME}/xena/xena.log
```

--------------------------------

### Add a cohort launch button

Source: https://ucsc-xena.gitbook.io/project/local-xena-hub/hubs-for-institutions-collaborations-labs-and-larger-projects.md

Use the cohortButton class to create a button that links to a specific bookmark or the visualization wizard.

```html
<button class="cohortButton" data-bookmark="bc7f3f46b042bcf5c099439c2816ff01">Example: compare FOXM1 expression</button>
```

--------------------------------

### Load data via command line

Source: https://ucsc-xena.gitbook.io/project/local-xena-hub/hubs-for-institutions-collaborations-labs-and-larger-projects.md

Load data files into the hub using the -l option. Specify the port with -p if the hub is not using the default 7222 port.

```bash
java -jar server.jar -l /path/to/root/file.tsv
```

```bash
java -jar server.jar -p ${PORT} -l /path/to/root/file.tsv
```

--------------------------------

### Configure Xena Hub data root directory

Source: https://ucsc-xena.gitbook.io/project/local-xena-hub/hubs-for-institutions-collaborations-labs-and-larger-projects.md

Sets the root directory for served data files, defaulting to ${HOME}/xena/files/.

```bash
--root -r default to ${HOME}/xena/files/
```

--------------------------------

### Load Data Files via Command Line

Source: https://ucsc-xena.gitbook.io/project/local-xena-hub/loading-data-from-the-command-line.md

Use the -l flag to load files from the specified directory. JSON metadata files are detected and loaded automatically.

```bash
java -jar cavm-0.xx.0-standalone.jar -l ~/xena/files/*
```

```bash
java -jar cavm-0.xx.0-standalone.jar -l ~/xena/files/file1.tsv
```

--------------------------------

### Create symbolic link for Xena server

Source: https://ucsc-xena.gitbook.io/project/local-xena-hub/hubs-for-institutions-collaborations-labs-and-larger-projects.md

Create a symbolic link to the standalone jar file to simplify command-line execution.

```bash
ln -sf cavm-x.xx.x-standalone.jar server.jar
```

--------------------------------

### Access Library Help

Source: https://ucsc-xena.gitbook.io/project/overview-of-features/accessing-data-through-python.md

Use the built-in Python help function to inspect the xenaPython library documentation.

```python
import xenaPython
help(xenaPython)
```

--------------------------------

### Download TOIL Manifest

Source: https://ucsc-xena.gitbook.io/project/faq/advanced-data-and-datasets.md

Use this command to download the TCGA manifest file from the S3 bucket.

```bash
aws s3 cp s3://cgl-rnaseq-recompute-toil/tcga-manifest . --request-pay
```

--------------------------------

### List Probemaps via Python

Source: https://ucsc-xena.gitbook.io/project/local-xena-hub/loading-data-from-the-command-line.md

Retrieve available probemap files using the xenaPython library.

```python
host =“https://reference.xenahubs.net”
xenaPython.probemap_list(host)
```

--------------------------------

### Import xenaPython

Source: https://ucsc-xena.gitbook.io/project/overview-of-features/accessing-data-through-python.md

Basic import statement for the xenaPython library.

```python
import xenaPython as xena
```

--------------------------------

### Add a Launch Xena Button to Landing Page

Source: https://ucsc-xena.gitbook.io/project/local-xena-hub/hubs-for-institutions-collaborations-labs-and-larger-projects.md

Include this button element in your hub's info.mdown file to trigger the Xena visualization wizard for a specific cohort.

```html
<button class="hubButton" data-cohort="TCGA TARGET GTEx">Launch Xena</button>
```

--------------------------------

### Link server jar

Source: https://ucsc-xena.gitbook.io/project/local-xena-hub/hubs-for-institutions-collaborations-labs-and-larger-projects.md

Creates a symbolic link to the standalone jar file.

```bash
ln -sf cavm-0.xx.0-standalone.jar server.jar
```

--------------------------------

### Constructing a Xena Deep Link URL

Source: https://ucsc-xena.gitbook.io/project/technical-documentation/deep-linking-into-xena.md

Demonstrates how to serialize a heatmap configuration object and append it to a Xena URL as an encoded query parameter.

```javascript
var heatmap_paramter = JSON.stringify({
      showWelcome: false,
      search: "B:=TARGET"
});
var url = page + ‘?columns=’ + encodeURIComponent(columns_parameter) + \
      ‘?heatmap=’ + encodeURIComponent(heatmap_paramter);
```

--------------------------------

### Constructing Xena Deep Links

Source: https://ucsc-xena.gitbook.io/project/technical-documentation/deep-linking-into-xena.md

Demonstrates the basic URL structure for linking to the Xena heatmap browser with encoded column and heatmap parameters.

```javascript
var page = ‘https://xenabrowser.net/heatmap/’;
var url = page + ‘?columns=’ + encodeURIComponent(columns_parameter) + \
    ‘&heatmap=’ + encodeURIComponent(heatmap_parameter);
```

--------------------------------

### Configure Apache as a Reverse Proxy for Xena Hub

Source: https://ucsc-xena.gitbook.io/project/local-xena-hub/hubs-for-institutions-collaborations-labs-and-larger-projects.md

Use this VirtualHost configuration in Apache to serve a Xena hub over HTTPS. Ensure the certificate and key files are correctly referenced.

```apache
<VirtualHost *:443>
    ServerName tcga.xenahubs.net
    SSLEngine on
    SSLProxyEngine On
    SSLProxyVerify none
    SSLProxyCheckPeerCN off
    SSLProxyCheckPeerName off
    SSLProxyCheckPeerExpire off
    SSLCertificateFile YOURCERTIFICATE
    SSLCertificateKeyFile YOURKEY
    # setup the proxy                                                                                                                                                                                          
    ProxyPreserveHost On
    ProxyPass / https://localhost:9000/
    ProxyPassReverse / https://localhost:9001/
</VirtualHost>
```

--------------------------------

### Generate Xena Deep Links with JavaScript

Source: https://ucsc-xena.gitbook.io/project/technical-documentation/deep-linking-into-xena.md

This script demonstrates how to construct URLs for the Xena browser by serializing column configurations into JSON and encoding them as URL parameters.

```html
<html>
<script>
	window.onload = function() {
        var browser = 'https://xenabrowser.net/';

        var hub1 = 'https://toil.xenahubs.net';
        var dataset1 = 'tcga_Kallisto_tpm';

		var hub2 = 'https://tcga.xenahubs.net';
		var dataset2 = 'TCGA.PANCAN.sampleMap/Gistic2_CopyNumber_Gistic2_all_data_by_genes';
		
		var hub3 = 'https://pancanatlas.xenahubs.net';
		var dataset3 = 'Survival_SupplementalTable_S1_20171025_xena_sp';

		var hub4 = 'https://pancanatlas.xenahubs.net';
		var dataset4 = 'broad.mit.edu_PANCAN_Genome_Wide_SNP_6_whitelisted.xena';

		var hub5 = 'https://gdc.xenahubs.net';
		var dataset5 = 'TCGA-BRCA.somaticmutation_wxs.tsv';

		var col1 = {name: dataset1, host: hub1, fields: 'TP53 FOXM1'};
		var col2 = {name: dataset2, host: hub2, fields: 'FOXM1'};
		var col3 = {name: dataset3, host: hub3, fields: 'cancer type abbreviation'};
		var col4 = {name: dataset4, host: hub4, fields: 'chr3:4000000-4100000'};
		var col5 = {
			name: dataset1,
			host: hub1,
			width: 400,
			columnLabel: 'top column label',
			fieldLabel: 'bottom column label',
			fields: 'ENST00000064780.6 ENST00000066544.7 ENST00000070846.10 ENST00000072516.7 ENST00000072644.5 ENST00000072869.8 ENST00000074304.9 ENST00000075120.11 ENST00000075322.10'
		};

		var col6 = {name: dataset1, host: hub1, fields: 'TP53'};
		var col6_geneAve = {name: dataset1, host: hub1, fields: 'TP53', geneAverage: true};

		var col7 = {name: dataset5, host: hub5, fields: 'TP53'};
		var col7_showIntron = {name: dataset5, host: hub5, fields: 'TP53', showIntrons: true};

		var col8 = {
			name: dataset1, 
			host: hub1, 
			fields: 'TP53 FOXM1', 
			sortDirection: 'reverse'
		};

		var heatmapChart = JSON.stringify({
			mode: 'chart'
		});

		var heatmapHideWelcome = JSON.stringify({
			showWelcome: false,
		});

		        var columns1 = JSON.stringify([col1]);
        var l1 = document.getElementById('link1');
        l1.href = browser + 'heatmap/?columns=' + encodeURIComponent(columns1);

        var columns2 = JSON.stringify([col1, col2]);
        var l2 = document.getElementById('link2');
        l2.href = browser + 'heatmap/?columns=' + encodeURIComponent(columns2) + '&heatmap=' + encodeURIComponent(heatmapChart);

        var columns3 = JSON.stringify([col3, col2, col4]);
        var l3 = document.getElementById('link3');
        l3.href = browser + 'heatmap/?columns=' + encodeURIComponent(columns3);

        var columns4 = JSON.stringify([col3, col5]);
        var l4 = document.getElementById('link4');
        l4.href = browser + 'heatmap/?columns=' + encodeURIComponent(columns4);

        var columns5 = JSON.stringify([col8]);
        var l5 = document.getElementById('link5');
        l5.href = browser + 'heatmap/?columns=' + encodeURIComponent(columns5);

        var columns6 = JSON.stringify([col6, col6_geneAve]);
        var l6 = document.getElementById('link6');
        l6.href = browser + 'heatmap/?columns=' + encodeURIComponent(columns6);

        var columns7 = JSON.stringify([col7, col7_showIntron]);
        var l7 = document.getElementById('link7');
        l7.href = browser + 'heatmap/?columns=' + encodeURIComponent(columns7) + '&heatmap=' + encodeURIComponent(heatmapHideWelcome);
    };
</script>
<body>
    <a id=link1>Example 1</a> One data column (with two subcolumns) display
	<br><br>
	<a id=link2>Example 2</a> Display in chart mode
	<br><br>
	<a id=link3>Example 3</a> Three data column display, one clinical data column, two genomic data columns
	<br><br>
	<a id=link4>Example 4</a> Specify column width, top label, and bottom label on Column C
	<br><br>
	<a id=link5>Example 5</a> Reverse sort on Column B
	<br><br>
	<a id=link6>Example 6</a> Display gene average in Column C
	<br><br>
	<a id=link7>Example 7</a> Display introns in Column C; Hide welcome banner
</body>
</html>
```

--------------------------------

### Establish SSH tunnel for hub access

Source: https://ucsc-xena.gitbook.io/project/local-xena-hub/hubs-for-institutions-collaborations-labs-and-larger-projects.md

Use SSH tunneling to access a remote hub when a security certificate is not configured. The first command shows standard login, the second establishes the tunnel.

```bash
ssh -i "xena.pem" ec2-user@ec2-11-111-11-111.compute-1.amazonaws.com
```

```bash
ssh -i "xena.pem" -L 8000:localhost:7222 ec2-user@ec2-11-111-11-111.compute-1.amazonaws.com
```

--------------------------------

### Download Single TOIL File

Source: https://ucsc-xena.gitbook.io/project/faq/advanced-data-and-datasets.md

Use this command to download a specific tar.gz file from the TCGA dataset.

```bash
aws s3 cp s3://cgl-rnaseq-recompute-toil/tcga/0106d51d-d581-4be7-91f3-b2f0c84468d1.tar.gz . --request-pay
```

--------------------------------

### Constructing the columns parameter

Source: https://ucsc-xena.gitbook.io/project/technical-documentation/deep-linking-into-xena.md

Create a JSON-encoded string representing the columns to display and append it to the Xena page URL.

```javascript
var column = {name: dataset1, host: hub1, fields: 'foo bar'};
var columns_parameter = JSON.stringify([column]);
var url = page + ‘?columns=’ + encodeURIComponent(columns_parameter);
```

--------------------------------

### Define a spatial map with microscopy images

Source: https://ucsc-xena.gitbook.io/project/technical-documentation/metadata-specification-1.md

Configure a spatial map by providing unit, spot diameter, and image path details.

```json
{
    "type": "clinicalMatrix",
    "cohort": "name of the cohort",
    "label": "display label of the file",
    "dataSubType": "the section the dataset is displayed under in Xena Datapages, describe what data is in the life",
    "map": [
    {
        "label": "display label of the map",
        "dataSubType": "spatial",
        "dimension": ["X","Y"],
        "unit": "pixel",
        "spot_diameter": 178.37655999999998,
        "micrometer_per_unit": 0.3083364764966877,
        "image": [
            {
            "label": "display label of the image",
            "path": "image file path",
            "size": [24240, 24240],
            "offset": [0,0],
            "image_scalef": 1,
            },
            {
            "label": "display label of the image",
            "path": "image file path",
            "size": [2000, 2000],
            "offset": [0,0],
            "image_scalef": 0.08250825
            }]
      }]
}
```

--------------------------------

### Metadata with Cohort

Source: https://ucsc-xena.gitbook.io/project/local-xena-hub/loading-data-from-the-command-line.md

JSON metadata file including both the data type and the specific cohort name.

```json
{"type":"mutationVector", 
 "cohort":"TCGA Breast Cancer"}
```

--------------------------------

### Probemap Metadata File

Source: https://ucsc-xena.gitbook.io/project/local-xena-hub/loading-data-from-the-command-line.md

Required metadata file for a probemap, placed in the same directory as the probemap file.

```json
{ “type”:“probeMap”, 
  “assembly”:“hg19"}
```

--------------------------------

### Delete Data Files via Command Line

Source: https://ucsc-xena.gitbook.io/project/local-xena-hub/loading-data-from-the-command-line.md

Use the -x flag to remove specific data files from the system.

```bash
java -jar cavm-0.xx.0-standalone.jar -x ~/xena/files/file1.tsv
```

```bash
java -jar cavm-0.xx.0-standalone.jar -x ~/xena/files/file1.tsv ~/xena/files/file2.tsv
```

--------------------------------

### Metadata Type Definition

Source: https://ucsc-xena.gitbook.io/project/local-xena-hub/loading-data-from-the-command-line.md

Minimal JSON metadata file specifying only the data type.

```json
{"type":"mutationVector"}
```

--------------------------------

### Define a spatial map with microscopy and transcript data

Source: https://ucsc-xena.gitbook.io/project/technical-documentation/metadata-specification-1.md

Include transcript data paths and dimensions alongside spatial image information.

```json
{
    "type": "clinicalMatrix",
    "dataSubtype": "phenotype",
    "label": "display label of the file",
    "cohort": "name of the cohort",
    "bioentity":"cell",
    "map":[
        {
            "label":"mIF H&E coregistered",
            "type":"spatial",
            "dimension":["CenterX", "CenterY"],
            "unit":"pixel",
            "micrometer_per_unit":0.120280945,
            "spot_diameter":84,
            "image":[
                {
                    "label":"morphology 2D image, coregistered H&E",
                    "path":"/CosMx/img",
                    "offset": [0, 0],
                    "image_scalef": 1
                }
            ],
            "transcript":[
                {
                    "label":"CosMx transcript data",
                    "path":"transcripts.tsv",
                    "dimension":["x","y"]
		}
            ]
        }
    ]
}
```

--------------------------------

### Metadata with Reference Genome

Source: https://ucsc-xena.gitbook.io/project/local-xena-hub/loading-data-from-the-command-line.md

JSON metadata file for mutation or segmented data requiring an assembly reference.

```json
{"type":"mutationVector", 
 "cohort":"TCGA Breast Cancer", 
 "assembly":"hg19"}
```

--------------------------------

### Define clinical feature attributes

Source: https://ucsc-xena.gitbook.io/project/technical-documentation/metadata-specification-1.md

Create a tab-delimited file to define feature attributes such as valueType, state, and stateOrder.

```text
feature    attribute    value
alcohol_history    valueType    category
alcohol_history    state    no
alcohol_history    state    yes
alcohol_history_intensity    stateOrder    "no","yes"
```

--------------------------------

### heatmap parameter

Source: https://ucsc-xena.gitbook.io/project/technical-documentation/deep-linking-into-xena.md

The heatmap parameter is a JSON-encoded object that allows users to configure global display settings, search for samples, and filter data views via URL.

```APIDOC
## heatmap parameter

### Description
The heatmap parameter is a JSON-encoded object specifying global display options for the Xena view.

### Properties
- **mode** (string) - Set to 'chart' to display in chart mode.
- **showWelcome** (boolean) - Toggle the welcome banner.
- **searchSampleList** (array) - List of strings to highlight specific samples.
- **search** (string) - Highlight samples based on a search expression.
- **filter** (string) - Filter the view to samples matching the expression.

### Usage Example
```javascript
var heatmap_paramter = JSON.stringify({
      showWelcome: false,
      search: "B:=TARGET"
});
var url = page + '?columns=' + encodeURIComponent(columns_parameter) + 
      '?heatmap=' + encodeURIComponent(heatmap_paramter);
```
```

--------------------------------

### columns parameter

Source: https://ucsc-xena.gitbook.io/project/technical-documentation/deep-linking-into-xena.md

The columns parameter is a JSON-encoded array of objects used to define the data columns displayed in the Xena interface.

```APIDOC
## columns parameter

### Description
The columns parameter is a JSON-encoded array of objects, specifying the columns to display in the Xena visualization. It is passed as a query parameter in the URL.

### Properties
- **name** (string) - Required - The dataset ID.
- **host** (string) - Required - The hub where the data resides.
- **fields** (string) - Required - The fields to display (gene, probe, or chromosome position).

### Optional Properties
- **width** (number) - Optional - Width in pixels.
- **columnLabel** (string) - Optional - Text for top column label.
- **fieldLabel** (string) - Optional - Text for bottom column label.
- **geneAverage** (boolean) - Optional - Display the gene average instead of individual probes.
- **normalize** (string) - Optional - Dynamic normalization: 'none', 'mean', 'log2', or 'normal2'.
- **showIntrons** (boolean) - Optional - Show introns for mutation and segmented copy number columns.
- **sortDirection** (string) - Optional - Set to 'reverse' to reverse sort the samples.
- **sortVisible** (boolean) - Optional - Sort column on the zoomed region.

### Usage Example
```javascript
var column = {name: 'dataset1', host: 'hub1', fields: 'foo bar'};
var columns_parameter = JSON.stringify([column]);
var url = page + '?columns=' + encodeURIComponent(columns_parameter);
```
```

--------------------------------

### Reference clinical feature file in phenotype metadata

Source: https://ucsc-xena.gitbook.io/project/technical-documentation/metadata-specification-1.md

Add a clinicalFeature reference to the phenotype file's JSON metadata using the colon notation.

```json
{
    "cohort": "TCGA Breast Cancer (BRCA)",
    "label": "label of you dataset", 
    "type": "clinicalMatrix",
    ":clinialFeature": "clinicalFeature.txt"
}
```

--------------------------------

### Define a clinical matrix map without an image

Source: https://ucsc-xena.gitbook.io/project/technical-documentation/metadata-specification-1.md

Use this structure to define a basic clinical matrix map with specified dimensions.

```javascript
{
    "type": "clinicalMatrix",
    "cohort": "name of the cohort",
    "label": "display label of the file",
    "dataSubType": "the section the dataset is displayed under in Xena Datapages, describe what data is in the life",
    "map": [
      {
        "label": "display label of the map",
        "dataSubType": "embedding",
        "dimension": ["UMAP_1","UMAP_2","UMAP_3"] 
      }
    ]
}
```

--------------------------------

### Define survival time units in metadata

Source: https://ucsc-xena.gitbook.io/project/technical-documentation/metadata-specification-1.md

Specify the units for survival endpoints like OS, DSS, DFI, and PFI within the clinicalMatrix metadata JSON.

```json
{
    "cohort": "TCGA Breast Cancer (BRCA)", 
    "dataSubType": "phenotype", 
    "label": "Curated survival data", 
    "type": "clinicalMatrix", 
    "units": {
        "OS": "days",
        "DSS": "days",
        "DFI": "days",
        "PFI": "days"
    }
}
```

--------------------------------

### filterColumns parameter

Source: https://ucsc-xena.gitbook.io/project/technical-documentation/deep-linking-into-xena.md

The filterColumns parameter allows users to specify columns that are used for sample filtering without being displayed in the visualization.

```APIDOC
## filterColumns parameter

### Description
This parameter defines columns that are available for sample filtering but are not displayed in the visual spreadsheet. These columns are referenced semantically after the columns defined in the 'columns' parameter.
```

--------------------------------

### Define clinical feature metadata

Source: https://ucsc-xena.gitbook.io/project/technical-documentation/metadata-specification-1.md

Specify the type as clinicalFeature in the JSON file accompanying the clinical feature text file.

```json
{
    "type":"clinicalFeature"
}
```

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