> For the complete documentation index, see [llms.txt](https://docs.biobox.io/guide/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.biobox.io/guide/how-to/ask-multi-modal-questions/ask-questions-with-query-language/visualize-data-returned-in-query-language.md).

# Visualize data returned in Query Language

Once you have used the query language to ask a question you can select from a variety of plots to visualize your data. 

## Scatter Plot

Any concept or relationship that contains numerical data properties can be visualized within a scatter  plot. 

Select "Add Visualization" followed by scatter plot. 

<figure><img src="/files/aw4aXhgryfT8VP7pHFPj" alt=""><figcaption><p>Example query " Which genes are upregulated in adenocarcinoma tumor samples?" This returned a list of 453 genes that were identified to be upregulated.</p></figcaption></figure>

<figure><img src="/files/1kFqBX4TQdaL4CylRlNJ" alt=""><figcaption></figcaption></figure>

The plot will populate below the table displaying the response to your query.&#x20;

### Plot Customization

Under the"Axis" menu you can customize the data that will be displayed and axis labels&#x20;

* "**X Axis Concept**" refers to the concept or relationship from your query that will be displayed on the X axis e.g. upregulates, gene, tumor sample etc. Note that only concepts and relationships with numerical data properties will be available.
* "**X-Axis Property"** refers to the data property that will be displayed in the plot e.g. logR value, p value, etc.&#x20;
* "**X-Axis Label**" refers to the title of the X-Axis.
* "**Y-Axis Concept**" refers to the concept or relationship from your query that will be displayed in the plot e.g. upregulates, gene, tumor sample etc. Note that only concepts and relationships with numerical data properties will be available.
* "**Y-Axis Property"** refers to the data property that will be displayed on the Y axis e.g. logR value, p value, etc.&#x20;
* "**Y-Aixs label"** refers to the title of the Y-Axis.&#x20;

<figure><img src="/files/UkeQlOL2s4Z7bpC4dh17" alt=""><figcaption></figcaption></figure>

To provide additional context tool tips can be added. This allows you to display additional information when hovering over data points such as Gene Names.&#x20;

<figure><img src="/files/dkMNIJb263B4FJtM7mQn" alt=""><figcaption></figcaption></figure>

By default, the query will be the title of the plot. This can be changed under the Title and Grid menu.&#x20;

<figure><img src="/files/CO76eXttQOnSn4JA7M5f" alt=""><figcaption></figcaption></figure>

<figure><img src="/files/M8E33M19EC57PbdKxntr" alt=""><figcaption></figcaption></figure>

The horizontal and vertical sliders can be used to zoom in and out of the plot.&#x20;

## Box Plot

Select "Add Visualization" followed by Box plot.&#x20;

<figure><img src="/files/H3CKjIHVsg6xoGH1hLle" alt=""><figcaption><p>Example query "Which genes that participate in the Activation of BH3-only proteins are upregulated across differential expression datasets" This returned 28 genes identified across 4 differential expression datasets. </p></figcaption></figure>

The plot will populate below the table displaying the response to your query.&#x20;

### Plot Customization

Under the"Axis" menu you can customize the data that will be displayed and axis labels&#x20;

* "**X Axis concept**" refers to the concept or relationship from your query that will be displayed on the X-axis e.g gene, tumor sample, dataset etc.&#x20;
* "**X-Axis Property"** refers to the data property that will be displayed in the plot e.g. gene name dataset name, p value, etc.&#x20;
* "**X-Axis Label**" refers to the title of the X-Axis.&#x20;
* "**Y-Axis concept**" refers to the concept or relationship from your query that will be displayed in the plot e.g. upregulates, gene, tumor sample etc. Note that only concepts and relationships with numerical data properties will be available.
* "**Y-Axis Property"** refers to the data property that will be displayed in the plot e.g. logR value, p value, etc.&#x20;
* "**Y-Axis Label"** refers to the title of the Y-Axis.&#x20;

<figure><img src="/files/B2iUdylNSZhr3aYkKTle" alt=""><figcaption></figcaption></figure>

By default, the query will be the title of the plot. This can be changed under the Title and Grid menu.

<figure><img src="/files/oG3B32bUdzDcNK4oanxL" alt=""><figcaption></figcaption></figure>

<figure><img src="/files/UkQsnBZenpqt5YPbKYKX" alt=""><figcaption></figcaption></figure>

The horizontal and vertical sliders can be used to zoom in and out of the plot.&#x20;


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter:

```
GET https://docs.biobox.io/guide/how-to/ask-multi-modal-questions/ask-questions-with-query-language/visualize-data-returned-in-query-language.md?ask=<question>&goal=<endgoal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.