diff --git a/docs/pecan/expression/index.md b/docs/pecan/expression/index.md index b1090d07..e793ff2c 100644 --- a/docs/pecan/expression/index.md +++ b/docs/pecan/expression/index.md @@ -40,5 +40,5 @@ Further, the lasso enables a user to select a region on the plot to enable furth **Figure 3: Lasso.** A user can use the lasso feature to populate a table to retrieve a list of sampleIDs for the selected region. !!!warning -Filtering by the sunburst will autopopulate the search with a specific key. A user can remove the text or click the subtypes on the right to continue exploring. +Filtering by the sunburst will auto-populate the search with a specific key. A user can remove the text or click the subtypes on the right to continue exploring. !!! \ No newline at end of file diff --git a/docs/pecan/histology/index.md b/docs/pecan/histology/index.md index 9e30653d..263f27e5 100644 --- a/docs/pecan/histology/index.md +++ b/docs/pecan/histology/index.md @@ -2,7 +2,7 @@ title: Histology --- ![Histology](./../histology.svg) -**Overview:** Explore over 400 histology slides (H&E stained) that have been harmonized to our ontology disease hierarchy. *The remaining COMET slides are pending publication.* +**Overview:** Explore ~400 histology slides (H&E stained) that have been harmonized to our ontology disease hierarchy. *The remaining COMET slides are pending publication.* **ADVANCED SEARCH** - The Histology homepage (**Figure 1**) will comprise an advanced search page enabling filtering of slides via metadata--diagnosis, subtype, sex, age, site, evaluation, site classification-- via drop-down lists. The return provides thumbnails with minimum data about the slide (e.g., subtype, sex, age, and SJID). Sample IDs can be searched individually. @@ -23,11 +23,17 @@ This view (**Figure 2**) enables access to each histology slide via a “sample This view (**Figure 3**) enables the exploration of a sample slide via a slide image viewer page supported by OpenSeaDragon (feature listed below). **Features:** + *Home*: refreshes the slide to the original state + *Magnify+*: Zoom in + *Magnify-*: Zoom out + *Rotate left*: rotates slide left by 90 degrees + *Rotate right*: rotates slide right by 90 degrees + *Slidescale*: scale shows dimension ![](./slide_viewer.png) diff --git a/docs/pecan/variants/index.md b/docs/pecan/variants/index.md index e1ac936f..4ccb1762 100644 --- a/docs/pecan/variants/index.md +++ b/docs/pecan/variants/index.md @@ -20,7 +20,7 @@ Updating the filters will **not** update the sunburst selection, but it **will** !!! ![](./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. +**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. !!!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. @@ -69,7 +69,7 @@ The user will be given a GenomePaint view, supported by ProteinPaint, for all of Or, the user can filter the view based on the selected subtype (**Figure 7**). -![](./genomepaint_moreinfo.png) +![](./genomepaint_filtering.png) **Figure 7. GenomePaint view, with filtering.** This visualization will provide the basic GenomePaint view where the reference genome, Pediatric dataset, and the selected subtype data will show.