Skip to content

Commit

Permalink
Merge pull request #128 from stjudecloud/expression/update-images
Browse files Browse the repository at this point in the history
Gene expression text and image updates
  • Loading branch information
jsunny23 authored Oct 25, 2024
2 parents 8bf86ac + b6fd1ed commit 6eba60d
Show file tree
Hide file tree
Showing 11 changed files with 13 additions and 12 deletions.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
25 changes: 13 additions & 12 deletions docs/pecan/expression/index.md
Original file line number Diff line number Diff line change
Expand Up @@ -6,16 +6,17 @@ title: Expression

This facet comprises three tabs, allowing users to explore the expression landscape of 3,432 RNA-Seq fresh frozen tumor samples (1,389 blood tumors, 888 solid tumors, and 1,155 brain tumors) using a t-SNE plot (**Figure 1**), gene expression violin plots organized by subtype for a gene of interest (**Figure 2**), gene expression overlayed on the t-SNE, or collectively within a data matrix.

[NEED NEW IMAGE]
![](./expression-t-sne-initial-screen.png)
![](./expression-t-sne-sample-view.png)

**Figure 1: t-SNE for Blood, Brain, and Solid Samples.** Mouse over data points to access metadata details for each sample. Visualization powered by D3.

[NEED NEW IMAGE]
![](./expression-gene-violin-plots.png)

**Figure 2: Gene Expression for TP53.** Gene expression violin plots for each sample, filtered by the gene of interest. Visualization powered by Plotly.
**Figure 2: Gene Expression for MYCN.** Gene expression violin plots for each sample, filtered by the gene of interest. Visualization powered by Plotly.

> **Note**
> - All samples use the hg38 reference genome.
> **Note**
> - All samples use the hg38 reference genome.
> - Full metadata can be accessed through our [manifest](https://platform.stjude.cloud/api/v1/manifest).
---
Expand All @@ -31,9 +32,9 @@ This facet comprises three tabs, allowing users to explore the expression landsc
| **Lasso Tool** | Select a region on the plot to retrieve a list of samples for further investigation. |
| **Pan/Zoom** | Zoom in or pan to examine specific regions of the plot. This will disable subtype labels. |

[NEED NEW GIF]
![](./expression-t-sne-features-overview.gif)

> **Warning**
> **Warning**
> Filtering by the sunburst will auto-populate the Root and Subtype filters. These can be manually edited but will not update the sunburst.
---
Expand All @@ -49,22 +50,22 @@ This facet comprises three tabs, allowing users to explore the expression landsc

For data normalization details, refer to our [Methods and Data](https://university.stjude.cloud/docs/pecan/methods-data/) page.

[NEED NEW GIF]
![](./expression-violin-plots.gif)
---

## Gene Expression Overlay on t-SNE

Users can overlay gene expression on the t-SNE plot by selecting genes of interest. Count data is normalized using Median of Ratios (MoR). More details can be found on the [Methods and Data](https://university.stjude.cloud/docs/pecan/methods-data/) page.

[NEED NEW GIF]
![](./expression-gene-expression-toggle.gif)

---

## Features for the Data Matrix

The data matrix displays all filtered data with sortable headers for easier exploration.

[NEED NEW GIF]
![](./expression-data-sortable-columns.gif)

---

Expand Down Expand Up @@ -96,10 +97,10 @@ The data matrix displays all filtered data with sortable headers for easier expl
| **Library Selection Protocol** | Multi-select dropdown for library protocol types. |
| **Preservative** | Multi-select dropdown for sample preservative types. |

> **Warning**
> **Warning**
> Some fields may have a "Not Available" option for samples where the data wasn't recorded (e.g., Race, Ethnicity, Sex).
> **Tip**
> **Tip**
> For a subset of this data, refer to [Figure 4f of McLeod et al.](https://cancerdiscovery.aacrjournals.org/content/11/5/1082.long)
---
Expand Down

1 comment on commit 6eba60d

@github-actions
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Please sign in to comment.