feat: oncoprint and june release notes

content/4.pecan/2.data-facets/1.variants.md

@@ -8,49 +8,9 @@ title: Variants
 Perform exploratory research of variants in pediatric cancer subtypes via 5 custom interactive interfaces.
 Curated variants have been identified from whole-genome, whole-exome and whole-transcriptome (RNA-seq) sequencing data from 5500 samples.
 
-## ONCOPRINT
-
-A user will default to a placeholder if a diagnosis and/or subtype is not selected from the Sunburst (**Figure 1**).
-
-![oncoprint](/img/pecan/data-facets/variants/oncoprint.png)
-
-**Figure 1: Variants: Oncoprint view, without filtering.**
-A placeholder is shown when a user directly accesses the Variants data facet.
-
-Diagnosis and/or subtype is required for generating a new oncoprint (**Figure 2**).
-
-::callout{icon="i-heroicons-exclamation-circle" color="orange"}
-**Warning**  
-Updating the filters will **not** update the Sunburst selection, but it **will** update the other facet views (e.g., Variant Prevalence, GenomePaint, and/or ProteinPaint).
-::
-
-![oncoprint template](/img/pecan/data-facets/variants/oncoprint_template.png)
-
-**Figure 2: Variants: Oncoprint view, with filtering.**
-This figure can be generated by following the subtype-centric user experience where a (i) diagnosis and/or subtype was selected from the Sunburst landing page or (ii) a user selected a diagnosis and/or subtype filter -- the filters on the left will auto-populate based on the Sunburst filter selection and can later be customized.
-
-::callout{icon="i-heroicons-light-bulb" color="blue"}
-**Tip**  
-
-- The oncoprint is generated by ProteinPaint and therefore if a user alters the configs within the ProteinPaint UI (e.g, settings, sort, data, etc), the filters will not update, nor will PeCan save this state in the membrane.
-- Clicking a gene will enable a button that allows the user to navigate to ProteinPaint or GenomePaint for that gene.
-::
-
-Once the filters are selected and submitted, then an oncoprint will render.
-For example, a user can choose to render an oncoprint for just a disease: [Brain](https://pecan.stjude.cloud/variants/oncoprint/BT), [Solid](https://pecan.stjude.cloud/variants/oncoprint/ST), or [Blood(Heme)](https://pecan.stjude.cloud/variants/oncoprint/HM).
-Further, the user can customize the oncoprint by employing the ProteinPaint [settings](https://docs.google.com/document/d/1bx3VRdTzJDYdmt4CaU4PfHCOz5JSfTyuSFIuGTx-X2g/).
-
-A few highlights to mention about the ProteinPaint configs are described below (**Figure 3**).
-
-![oncoprint proteinpaint](/img/pecan/data-facets/variants/oncoprint_proteinpaint.png)
-
-**Figure 3: Oncoprint configs.**
-ProteinPaint's UI has customizable configurations that enable a user to edit and change the visualization.
-
 ## VARIANT PREVALENCE
 
-Selected diagnoses within the third ring of the Sunburst have curated  driver variants assigned to pathways.
-For these cases the variant prevalence page will be headed by a vertically stacked bar plot: the mutational prevalence summary.
+Mutational prevalence summaries are available for higher-level subtype nodes such as Hematological Malignancy, Lymphoid Neoplasm, and Myeloid Neoplasm. At higher-level subtype nodes, pathway prevalence summary is segmented by immediate child diseases. At lower-level disease nodes, pathway prevalence is segmented by all descendant leaf subtypes.
 [For methods details follow this link](/pecan/overview/methods-and-data).
 
 ### Mutational Prevalence Summary
@@ -147,7 +107,7 @@ See our [Methods and Data](/pecan/overview/methods-and-data) section to learn mo
 
 **Figure 11.**
 ProteinPaint view, without filtering.
-This visualization will provide the basic ProteinPaint view where the full `Pediatric` dataset defaults to hg19.
+This visualization will provide the basic ProteinPaint view where the full `Pediatric` dataset defaults to hg38.
 
 When the user filters by diagnosis and/or subtype, the user will see a subset of data underneath the full `Pediatric` dataset (**Figure 12**).
 
@@ -190,6 +150,43 @@ Then, click the `pathogenic` or `likely pathogenic` button to access the variant
 If there are more variant changes at the same coordinate, a user can hover under the bottom variant and find a total which creates the variant table for all variants at that amino acid (*as seen in Figure 11*).
 ::
 
+## ONCOPRINT
+
+A user will default to a placeholder if a diagnosis and/or subtype is not selected from the Subtype Search or Subtype Tree (**Figure 1**).
+
+![oncoprint](/img/pecan/data-facets/variants/oncoprint.png)
+
+**Figure 1: Variants: Oncoprint view, without filtering.**
+A placeholder is shown when a user directly accesses the Variants data facet.
+
+Diagnosis and/or subtype is required for generating a new oncoprint (**Figure 2**).
+
+::callout{icon="i-heroicons-exclamation-circle" color="orange"}
+**Warning**  
+Updating the filters will **not** update the Subtype Search or Subtype Tree selection, but it **will** update the other facet views (e.g., Variant Prevalence, GenomePaint, and/or ProteinPaint).
+::
+
+![oncoprint template](/img/pecan/data-facets/variants/oncoprint_template.png)
+
+**Figure 2: Variants: Oncoprint view, with filtering.**
+This figure can be generated by following the subtype-centric user experience where a (i) diagnosis and/or subtype was selected from the Subtype Search or Subtype Tree landing page or (ii) a user selected a diagnosis and/or subtype filter -- the filters on the left will auto-populate based on the Subtype Search or Subtype Tree selection and can later be customized.
+
+::callout{icon="i-heroicons-light-bulb" color="blue"}
+**Tip**  
+
+- Clicking a gene will enable a button that allows the user to navigate to ProteinPaint or GenomePaint for that gene.
+::
+
+Once the filters are selected and submitted, then an oncoprint will render.
+For example, a user can choose to render an oncoprint for just a disease: [Brain](https://pecan.stjude.cloud/variants/oncoprint/BT), [Solid](https://pecan.stjude.cloud/variants/oncoprint/ST), or [Blood(Heme)](https://pecan.stjude.cloud/variants/oncoprint/HM).
+
+A few highlights to mention about the configs are described below (**Figure 3**).
+
+![oncoprint](/img/pecan/data-facets/variants/oncoprint_navigation.png)
+
+**Figure 3: Oncoprint configs.**
+Controls are available to **Drag and Drop, Sort and Filter** samples or metadata within the heatmap.
+
 ## VARIANT DETAILS
 
 A user can access variant details (**Figure 15**) which are individual customized variant pages displaying detailed associated genomic, clinical, classification, and observed population frequency annotation.

content/4.pecan/5.release-notes/1.index.md

@@ -7,6 +7,24 @@ description: A running changelog for the PeCan project.
 
 Hi there! Welcome to the PeCan Release Notes page. Here, you'll find a running log of new features, improvements, and changes we've made to PeCan—along with a bit of the rationale behind why we're making them. Check back after each release to see what's new! If you have any questions, feel free to reach out to us at [support@stjude.cloud](mailto:support@stjude.cloud).
 
+## June 2026
+
+This release updates Oncoprint to align visually with the rest of PeCan and adds new features for exploring mutation data by diagnosis subtype.
+
+### Oncoprint
+
+- **Visual Alignment:** Mutation colors now match the Variant Prevalence data facet, making it easier to recognize mutation types across views.
+- **Row Configuration:** Rows in the Oncoprint can be reordered by drag-and-drop, or sorted and filtered.
+- **Navigator Panel:** A new panel at the bottom of the view supports navigation across larger cohorts of samples.
+
+### Variants
+
+- **Variant Prevalence** Mutational prevalence summaries are now available for higher-level subtype nodes such as Hematological Malignancy, Lymphoid Neoplasm, and Myeloid Neoplasm.  At higher-level subtype nodes, pathway prevalence summary is segmented by immediate child diseases. At lower-level disease nodes, pathway prevalence is segmented by all descendant leaf subtypes.
+
+### ProteinPaint & GenomePaint
+
+- Both tools now default to hg38
+
 ## May 2026
 
 This release introduces our Subtype Tree to PeCan, a new way to explore and navigate the full [CC4K](https://docs.stjude.cloud/cc4k) hierarchy of pediatric cancer diagnoses across St. Jude Cloud data.