diff --git a/src/App.css b/src/App.css index 4858ac9f..abfd3a03 100644 --- a/src/App.css +++ b/src/App.css @@ -1245,6 +1245,9 @@ a:hover { font-weight: 500; color: #469c77; } + span.text-green-alignment { + color: #5a9c7c; + } span.text-gray { color: #757575; } diff --git a/src/App.tsx b/src/App.tsx index 776fea61..bd468fc9 100644 --- a/src/App.tsx +++ b/src/App.tsx @@ -323,10 +323,6 @@ function App(props: RouteComponentProps) { }, 500) ); - // Enable Bootstrap popovers for track tooltips - const popoverTriggerList = document.querySelectorAll('[data-bs-toggle="popover"]'); - const popoverList = [...popoverTriggerList].map(popoverTriggerEl => new bootstrap.Popover(popoverTriggerEl)); - // Lower opacity of legend image as it leaves viewport if (isMinimalMode) { const legendElement = document.querySelector('.genome-view-legend'); @@ -345,6 +341,13 @@ function App(props: RouteComponentProps) { } }, []); + // Enable Bootstrap popovers for track tooltips, update for selected SV tracks + useEffect(() => { + console.log('update popovers'); + const popoverTriggerList = document.querySelectorAll('[data-bs-toggle="popover"]'); + const popoverList = [...popoverTriggerList].map(popoverTriggerEl => new bootstrap.Popover(popoverTriggerEl)); + }, [selectedSvId]); + const getThumbnail = (d: SampleType) => { return ( d.thumbnail || diff --git a/src/ui/trackData.ts b/src/ui/trackData.ts index d0123b3f..6dd7e40e 100644 --- a/src/ui/trackData.ts +++ b/src/ui/trackData.ts @@ -385,18 +385,22 @@ export const getTrackDocData = (

Interpretation


+
+

The sequencing coverage track quantifies the number of sequencing reads covering each position.

+
+
- + Coverage track.
-

Sequencing coverage track quantifies the number of sequencing reads covering each position.

-

A vertical line denotes the breakpoint (if selected).

+

Black vertical dashed line - denotes the selected breakpoint.

+
- + Coverage, Sequence, and Alignment tracks.

Sequencing coverage is derived from the data on sequencing reads aligning to each position.

-

Black reads (those parts of reads that were split) do not contribute to the coverage sum.

+

Black reads - (those parts of reads that were split) do not contribute to the coverage sum.

@@ -404,7 +408,7 @@ export const getTrackDocData = (

Interactions


- + Coverage, Sequence, and Alignment tracks.

Click - on an SV to show its breakpoints in the read view.

@@ -423,9 +427,9 @@ export const getTrackDocData = (

Interpretation


- + Color legend for the Sequence track.
-

Colors represent DNA base-pairs in human reference genome.

+

Colors - represent DNA base-pairs in human reference genome.

@@ -442,22 +446,24 @@ export const getTrackDocData = (

Interpretation


- + Coverage, Sequence, and Alignment tracks.

Gray rectangles - denote normally-mapping reads.

Black rectangles - denote split reads, used as evidence for structural variants.

+
- + Green read colors in the Alignment track.
-

Other read colors (here, green) denote aberrantly mapping reads, which are also used as evidence for structural variants (see more info).

+

Other read colors (e.g. green) denote aberrantly mapping reads, which are also used as evidence for structural variants (see more info).

+
- + Black vertical dashed line in the Alignment track.
-

Vertical dashed line denotes a SV breakpoint.

+

Black vertical dashed line - denotes a SV breakpoint.

@@ -465,7 +471,7 @@ export const getTrackDocData = (

Interactions


- + ALignment track details pop up.

Hover - over a sequencing read to see more details.