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feat(pecan): gene expression added and methods and data updated
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| title: Expression | ||
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| ## Overview | ||
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| **Overview:** The expression landscape of 3432 RNA-Seq fresh frozen tumor samples (1389 blood tumors, 888 solid tumors, and 1155 brain tumors) in St. Jude Cloud is displayed via a t-SNE plot (**Figure 1**) generated using the [St. Jude Cloud RNA-Seq Expression Analysis workflow](https://platform.stjude.cloud/workflows/rnaseq-expression-classification). | ||
| 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. | ||
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| **Figure 1: tSNE for Blood, Brain, and Solid Samples.** Metadata details for each sample can be accessed by mousing over the data points. This visualization is supported by D3. | ||
| **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. | ||
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| !!!note | ||
| - All samples use the hg38 reference genome. | ||
| - All metdata can be found by accessing our [manifest](https://platform.stjude.cloud/api/v1/manifest) | ||
| !!! | ||
| [NEED NEW IMAGE] | ||
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| **Features:** | ||
| A user can explore across the 3 tSNE plots: Blood, Solid, or Brain tumor tabs and employ the features listed below: | ||
| **Figure 2: Gene Expression for TP53.** Gene expression violin plots for each sample, filtered by the gene of interest. Visualization powered by Plotly. | ||
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| *Subtype categorization*- Subtypes are denoted by a specific color and a subset have been labeled on the plot. | ||
| > **Note** | ||
| > - All samples use the hg38 reference genome. | ||
| > - Full metadata can be accessed through our [manifest](https://platform.stjude.cloud/api/v1/manifest). | ||
| *Sample Summary*- A user can select a data point on the plot that opens a sample summary drawer annotating relavent metadata and information. | ||
| --- | ||
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| ## Features for the t-SNE Plot | ||
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| | Feature | Description | | ||
| | -------------------------- | --------------------------------------------------------------------------------------------------------- | | ||
| | **Subtype Categorization** | Subtypes are color-coded, and a subset is labeled on the plot. These can be turned off in the 3 dot menu. | | ||
| | **Sample Summary** | Clicking a data point opens a drawer with metadata and sample details. | | ||
| | **Filters** | Filters are categorized by Tumor Sample, Patient Phenotype, and Sample Preparation. | | ||
| | **Sample Search** | Search by individual or bulk (comma-separated) sample IDs. CompBio IDs must be exact. | | ||
| | **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. | | ||
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| [NEED NEW GIF] | ||
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| > **Warning** | ||
| > Filtering by the sunburst will auto-populate the Root and Subtype filters. These can be manually edited but will not update the sunburst. | ||
| *Filters* - Filters are organized by Tumor Sample, Patient Phenotype, and Sample Preparation. Once a filter is selected, the subtype labels will be disabled. Functionality of each is further described below. | ||
| --- | ||
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| ## Features for Gene Expression | ||
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| *Sample Search* - A user can search individual sampleIDs or bulk IDs that are comma separated. The sampleIDs must be exact and cannot be fuzzy searched. | ||
| | Feature | Description | | ||
| | -------------------- | -------------------------------------------------------------------------------------------- | | ||
| | **Gene Sandbox** | Violin plots for the gene of interest, filtered by root and subtypes. | | ||
| | **Plotly Functions** | Pan and zoom features on the right side of the gene sandbox do not affect filter components. | | ||
| | **Median Sort** | Sort the gene expression sandboxes by median expression across or within individual groups. | | ||
| | **Outlier Toggle** | Toggle off data points to keep outliers intact for the cohort currently being filtered. | | ||
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| *Lasso* - Allows a user to select a specific region on the plot to retrieve a list of samples to enable further investigation. To view the sample summary of the lassoed samples, click the "Data" icon in the top right of the subnavbar. See GIF below. | ||
| For data normalization details, refer to our [Methods and Data](https://university.stjude.cloud/docs/pecan/methods-data/) page. | ||
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| *Pan/Zoom* - Allows a user to examine regions of the plot in more detail, this disables any labels. | ||
| [NEED NEW GIF] | ||
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| ## Gene Expression Overlay on t-SNE | ||
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| !!!warning | ||
| Filtering by the sunburst will auto-populate the diagnosis and subtype filter. A user can edit this modal, but it will not update the sunburst. | ||
| !!! | ||
| 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. | ||
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| **Filters Explained** | ||
| [NEED NEW GIF] | ||
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| --- | ||
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| ## Features for the Data Matrix | ||
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| The data matrix displays all filtered data with sortable headers for easier exploration. | ||
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| [NEED NEW GIF] | ||
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| --- | ||
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| ## Filters Explained | ||
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| ### Tumor Sample | ||
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| 1. Sample ID - A user can search individual St. Jude CompBio IDs or bulk search IDs that are comma separated. This field allows for a multi-select. | ||
| 2. Subtype - This is a modal whereby a user can custom select which subtypes to view in the plot. Child nodes will automatically become enabled or disabled if a parent node is (de)selected. The number of samples and the subtype color is desginated in the modal for reference. | ||
| 3. Subtype Biomarker - This field allows a multi-select of subtype biomarkers to be applied to the plot. *Note: the user cannot apply a general gene like "CTNNB1" to be applied across the plot. The user must select all biomarkers they are interested in seeing from the dropdown* | ||
| 4. Sample Type - This field is a multi-select dropdown. | ||
| | Filter | Description | | ||
| | --------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------- | | ||
| | **Sample ID** | Search by individual or bulk St. Jude CompBio IDs (comma-separated). Allows multi-select. | | ||
| | **Subtype Root** | Custom-select a root to prompt applicable subtypes. Heme is defaulted upon loading the facet unless the sunburst is employed. | | ||
| | **Subtype** | Custom-select subtypes to view on the plot. Parent node selection enables or disables child nodes. | | ||
| | **Subtype Biomarker** | Multi-select subtype biomarkers to apply on the plot. General genes like "CTNNB1" are not accepted; users must select biomarkers from dropdown. | | ||
| | **Sample Type** | Multi-select dropdown for sample types. | | ||
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| ### Patient Phenotype | ||
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| 1. Sex - A multi-select dropdown. | ||
| 2. Age at Diagnosis - A scale whereby a user can manually type in the age parameters or use the scale (in years). A user can type in any age, even passed our "35+" parameter. | ||
| 3. Race - This is a multi-select dropdown. | ||
| 4. Ethnicity - This is multi-select dropdown. | ||
| | Filter | Description | | ||
| | -------------------- | -------------------------------------------------- | | ||
| | **Sex** | Multi-select dropdown for biological sex. | | ||
| | **Age at Diagnosis** | Adjustable scale or manual input for age in years. | | ||
| | **Race** | Multi-select dropdown for race. | | ||
| | **Ethnicity** | Multi-select dropdown for ethnicity. | | ||
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| ### Sample Preparation | ||
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| 1. Library Selection Protocol - This is a multi-select dropdown. | ||
| 2. Preservative - This is a mutli-select dropwdown | ||
| | Filter | Description | | ||
| | ------------------------------ | ---------------------------------------------------- | | ||
| | **Library Selection Protocol** | Multi-select dropdown for library protocol types. | | ||
| | **Preservative** | Multi-select dropdown for sample preservative types. | | ||
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| > **Warning** | ||
| > Some fields may have a "Not Available" option for samples where the data wasn't recorded (e.g., Race, Ethnicity, Sex). | ||
| !!!warning | ||
| There can be fields with a "Not Available" option for samples that did not have this value recorded (e.g., Race, Ethnicity, Sex). | ||
| !!! | ||
| > **Tip** | ||
| > For a subset of this data, refer to [Figure 4f of McLeod et al.](https://cancerdiscovery.aacrjournals.org/content/11/5/1082.long) | ||
| --- | ||
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| !!!tip | ||
| An example with a subset of this data can be found in [Figure 4f of McLeod et al](https://cancerdiscovery.aacrjournals.org/content/11/5/1082.long). | ||
| !!! | ||
| To see how the data was calculated and normalized, visit our [Methods and Data](https://university.stjude.cloud/docs/pecan/methods-data/) page. | ||
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