diff --git a/docs/pecan/expression/expression-data-sortable-columns.gif b/docs/pecan/expression/expression-data-sortable-columns.gif new file mode 100644 index 0000000..f76a948 Binary files /dev/null and b/docs/pecan/expression/expression-data-sortable-columns.gif differ diff --git a/docs/pecan/expression/expression-gene-expression-toggle.gif b/docs/pecan/expression/expression-gene-expression-toggle.gif new file mode 100644 index 0000000..49656bf Binary files /dev/null and b/docs/pecan/expression/expression-gene-expression-toggle.gif differ diff --git a/docs/pecan/expression/expression-gene-violin-plots.png b/docs/pecan/expression/expression-gene-violin-plots.png new file mode 100644 index 0000000..7c98e9d Binary files /dev/null and b/docs/pecan/expression/expression-gene-violin-plots.png differ diff --git a/docs/pecan/expression/expression-gene-violin-plots@2x.png b/docs/pecan/expression/expression-gene-violin-plots@2x.png new file mode 100644 index 0000000..a605340 Binary files /dev/null and b/docs/pecan/expression/expression-gene-violin-plots@2x.png differ diff --git a/docs/pecan/expression/expression-t-sne-features-overview.gif b/docs/pecan/expression/expression-t-sne-features-overview.gif new file mode 100644 index 0000000..d62907b Binary files /dev/null and b/docs/pecan/expression/expression-t-sne-features-overview.gif differ diff --git a/docs/pecan/expression/expression-t-sne-initial-screen.png b/docs/pecan/expression/expression-t-sne-initial-screen.png new file mode 100644 index 0000000..085e363 Binary files /dev/null and b/docs/pecan/expression/expression-t-sne-initial-screen.png differ diff --git a/docs/pecan/expression/expression-t-sne-initial-screen@2x.png b/docs/pecan/expression/expression-t-sne-initial-screen@2x.png new file mode 100644 index 0000000..71b49de Binary files /dev/null and b/docs/pecan/expression/expression-t-sne-initial-screen@2x.png differ diff --git a/docs/pecan/expression/expression-t-sne-sample-view.png b/docs/pecan/expression/expression-t-sne-sample-view.png new file mode 100644 index 0000000..97d1b56 Binary files /dev/null and b/docs/pecan/expression/expression-t-sne-sample-view.png differ diff --git a/docs/pecan/expression/expression-t-sne-sample-view@2x.png b/docs/pecan/expression/expression-t-sne-sample-view@2x.png new file mode 100644 index 0000000..67b3546 Binary files /dev/null and b/docs/pecan/expression/expression-t-sne-sample-view@2x.png differ diff --git a/docs/pecan/expression/expression-violin-plots.gif b/docs/pecan/expression/expression-violin-plots.gif new file mode 100644 index 0000000..108a275 Binary files /dev/null and b/docs/pecan/expression/expression-violin-plots.gif differ diff --git a/docs/pecan/expression/index.md b/docs/pecan/expression/index.md index 113cb0d..4a13e09 100644 --- a/docs/pecan/expression/index.md +++ b/docs/pecan/expression/index.md @@ -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). --- @@ -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. --- @@ -49,14 +50,14 @@ 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) --- @@ -64,7 +65,7 @@ Users can overlay gene expression on the t-SNE plot by selecting genes of intere The data matrix displays all filtered data with sortable headers for easier exploration. -[NEED NEW GIF] +![](./expression-data-sortable-columns.gif) --- @@ -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) ---