Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Opacity of tracks based on a score/mappability #460

Open
wants to merge 4 commits into
base: master
Choose a base branch
from
Open

Opacity of tracks based on a score/mappability #460

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
25bf649
make nodes fully transparent again
jmonlong Aug 28, 2024
90cb8d4
add a checkbox to have read transparency by mapq
jmonlong Aug 28, 2024
93db207
update docker config
jmonlong Sep 10, 2024
5cf9051
Merge branch 'master' into color
jmonlong Oct 9, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions src/App.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -65,6 +65,7 @@ class App extends Component {
showReads: true,
showSoftClips: true,
colorReadsByMappingQuality: false,
alphaReadsByMappingQuality: false,
colorSchemes: getColorSchemesFromTracks(this.defaultViewTarget.tracks),
mappingQualityCutoff: 0,
},
Expand Down
12 changes: 12 additions & 0 deletions src/components/CustomizationAccordion.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -197,6 +197,18 @@ class VisualizationOptions extends Component {
Color reads by mapping quality
</Label>
</FormGroup>
<FormGroup check>
<Label check>
<Input
type="checkbox"
checked={visOptions.alphaReadsByMappingQuality}
onChange={() =>
toggleFlag("alphaReadsByMappingQuality")
}
/>
Transparency of reads by mapping quality
</Label>
</FormGroup>
<Form>
<Label className="mr-sm-2 " for="dataSourceSelect">
Mapping Quality Cutoff:
Expand Down
4 changes: 3 additions & 1 deletion src/components/HeaderForm.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -129,7 +129,9 @@ function tracksEqual(curr, next) {
curr_settings.mainPalette !== next_settings.mainPalette ||
curr_settings.auxPalette !== next_settings.auxPalette ||
curr_settings.colorReadsByMappingQuality !==
next_settings.colorReadsByMappingQuality
next_settings.colorReadsByMappingQuality ||
curr_settings.alphaReadsByMappingQuality !==
next_settings.alphaReadsByMappingQuality
) {
return false;
}
Expand Down
3 changes: 3 additions & 0 deletions src/components/TrackList.demo.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ export default (
mainPalette: "blues",
auxPalette: "reds",
colorReadsByMappingQuality: false,
alphaReadsByMappingQuality: false,
Comment on lines 18 to +19
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

If we're adding a new key to the color settings type we should update the schema we have here:

sequenceTubeMap/src/Types.ts

Line 85 in 0452ecb

colorReadsByMappingQuality: boolean

},
},
2: {
Expand All @@ -25,6 +26,7 @@ export default (
mainPalette: "blues",
auxPalette: "reds",
colorReadsByMappingQuality: false,
alphaReadsByMappingQuality: false,
},
},
3: {
Expand All @@ -34,6 +36,7 @@ export default (
mainPalette: "blues",
auxPalette: "reds",
colorReadsByMappingQuality: false,
alphaReadsByMappingQuality: false,
},
},
}),
Expand Down
3 changes: 3 additions & 0 deletions src/components/TrackList.test.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@ describe("TrackList", () => {
mainPalette: "blues",
auxPalette: "reds",
colorReadsByMappingQuality: false,
alphaReadsByMappingQuality: false,
},
},
2: {
Expand All @@ -21,6 +22,7 @@ describe("TrackList", () => {
mainPalette: "blues",
auxPalette: "reds",
colorReadsByMappingQuality: false,
alphaReadsByMappingQuality: false,
},
},
3: {
Expand All @@ -30,6 +32,7 @@ describe("TrackList", () => {
mainPalette: "blues",
auxPalette: "reds",
colorReadsByMappingQuality: false,
alphaReadsByMappingQuality: false,
},
},
};
Expand Down
1 change: 1 addition & 0 deletions src/components/TrackListItem.demo.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@ export default (
mainPalette: "blues",
auxPalette: "reds",
colorReadsByMappingQuality: false,
alphaReadsByMappingQuality: false,
},
}),
availableTracks: P.json([
Expand Down
1 change: 1 addition & 0 deletions src/components/TrackListItem.test.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@ describe("TrackListItem", () => {
mainPalette: "blues",
auxPalette: "reds",
colorReadsByMappingQuality: false,
alphaReadsByMappingQuality: false,
};

it("should render without errors", async () => {
Expand Down
3 changes: 3 additions & 0 deletions src/components/TrackPickerDisplay.demo.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ export default (
mainPalette: "blues",
auxPalette: "reds",
colorReadsByMappingQuality: false,
alphaReadsByMappingQuality: false,
},
},
2: {
Expand All @@ -25,6 +26,7 @@ export default (
mainPalette: "blues",
auxPalette: "reds",
colorReadsByMappingQuality: false,
alphaReadsByMappingQuality: false,
},
},
3: {
Expand All @@ -34,6 +36,7 @@ export default (
mainPalette: "blues",
auxPalette: "reds",
colorReadsByMappingQuality: false,
alphaReadsByMappingQuality: false,
},
},
}),
Expand Down
1 change: 1 addition & 0 deletions src/components/TrackPickerDisplay.test.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -174,6 +174,7 @@ describe("TrackPickerDisplay", () => {
mainPalette: "blues",
auxPalette: "reds",
colorReadsByMappingQuality: false,
alphaReadsByMappingQuality: false,
},
};

Expand Down
1 change: 1 addition & 0 deletions src/components/TrackSettings.demo.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@ export default (
mainPalette: "blues",
auxPalette: "reds",
colorReadsByMappingQuality: false,
alphaReadsByMappingQuality: false,
}),
availableColors: P.json([
"greys",
Expand Down
4 changes: 3 additions & 1 deletion src/components/TrackSettings.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,8 @@ import ColorPicker from "./ColorPicker";
* trackColorSettings expects an object in the form of
* {mainPalette: string,
* auxPallate: string,
* colorReadsByMappingQuality: boolean}
* colorReadsByMappingQuality: boolean,
* alphaReadsByMappingQuality: boolean}
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Maybe this should cross-reference the schema file https://github.com/vgteam/sequenceTubeMap/blob/0452ecb82d057372e359a9b456d789336e5ab8a1/src/Types.ts?

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Also, there's now two flags, which is a suspicious number of flags. We should think about redesigning this soon.

Really, the new alpha flag is the only one that ought to be a real flag, since it can be on or off and the main and aux palettes still matter.

If you turn on the color by mapping quality flag for a read track, the main and aux palettes are ignored. But keeping them around makes it easier to turn on color-by-MAPQ and then turn it off again and get back the same colors you had set.

*
* The setTrackColorSetting function expects to be passed a key value pair updating the trackColorSettings object
*
Expand Down Expand Up @@ -156,6 +157,7 @@ TrackSettings.defaultProps = {
mainPalette: "blues",
auxPalette: "reds",
colorReadsByMappingQuality: false,
alphaReadsByMappingQuality: false,
},
};

Expand Down
1 change: 1 addition & 0 deletions src/components/TrackSettings.test.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ describe("TrackSettings", () => {
mainPalette: "blues",
auxPalette: "reds",
colorReadsByMappingQuality: false,
alphaReadsByMappingQuality: false,
};

it("should render without errors", async () => {
Expand Down
1 change: 1 addition & 0 deletions src/components/TrackSettingsButton.demo.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@ export default (
mainPalette: "blues",
auxPalette: "reds",
colorReadsByMappingQuality: false,
alphaReadsByMappingQuality: false,
}),
availableColors: P.json([
"greys",
Expand Down
1 change: 1 addition & 0 deletions src/components/TrackSettingsButton.test.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@ describe("TrackSettingsButton", () => {
mainPalette: "blues",
auxPalette: "reds",
colorReadsByMappingQuality: false,
alphaReadsByMappingQuality: false,
}}
setTrackColorSetting={function (a, b) {}}
></TrackSettingsButton>
Expand Down
1 change: 1 addition & 0 deletions src/components/TubeMap.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,7 @@ class TubeMap extends Component {
let colorScheme = {
...visOptions.colorSchemes[key],
colorReadsByMappingQuality: visOptions.colorReadsByMappingQuality,
alphaReadsByMappingQuality: visOptions.alphaReadsByMappingQuality,
};
// update tubemap colors
tubeMap.setColorSet(key, colorScheme);
Expand Down
30 changes: 28 additions & 2 deletions src/util/tubemap.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2675,6 +2675,19 @@ function generateTrackColor(track, highlight) {
return trackColor;
}

function generateTrackAlpha(track, highlight) {
if (typeof highlight === "undefined") highlight = "plain";
let trackAlpha = 1;

const sourceID = track.sourceTrackID;
if (track.hasOwnProperty("type") && track.type === "read") {
if (config.colorSchemes[sourceID].alphaReadsByMappingQuality) {
trackAlpha = 0.1 + 0.9 * (Math.min(60, track.mapping_quality) / 60);
}
}
return trackAlpha;
}

function getReadXStart(read) {
const node = nodes[read.path[0].node];
if (read.path[0].isForward) {
Expand Down Expand Up @@ -2717,6 +2730,7 @@ function generateSVGShapesFromPath() {
let yStart;
let yEnd;
let trackColor;
let trackAlpha;
let highlight;
let dummy;
let reversalFlag;
Expand Down Expand Up @@ -2749,6 +2763,7 @@ function generateSVGShapesFromPath() {
tracks.forEach((track) => {
highlight = "plain";
trackColor = generateTrackColor(track, highlight);
trackAlpha = generateTrackAlpha(track, highlight);

// start of path
yStart = track.path[0].y;
Expand Down Expand Up @@ -2792,12 +2807,14 @@ function generateSVGShapesFromPath() {
}
if (xEnd !== xStart) {
trackColor = generateTrackColor(track, highlight);
trackAlpha = generateTrackAlpha(track, highlight);
trackRectangles.push({
xStart: Math.min(xStart, xEnd),
yStart,
xEnd: Math.max(xStart, xEnd),
yEnd: yStart + track.width - 1,
color: trackColor,
alpha: trackAlpha,
// TODO: This is not actually the index of the track!
id: track.id,
name: track.name,
Expand All @@ -2811,13 +2828,15 @@ function generateSVGShapesFromPath() {
xEnd = orderStartX[track.path[i].order];
yEnd = track.path[i].y;
trackColor = generateTrackColor(track, highlight);
trackAlpha = generateTrackAlpha(track, highlight);
trackCurves.push({
xStart,
yStart,
xEnd: xEnd + 1,
yEnd,
width: track.width,
color: trackColor,
alpha: trackAlpha,
laneChange: Math.abs(track.path[i].lane - track.path[i - 1].lane),
id: track.id,
name: track.name,
Expand All @@ -2833,13 +2852,15 @@ function generateSVGShapesFromPath() {
xEnd = orderEndX[track.path[i].order];
yEnd = track.path[i].y;
trackColor = generateTrackColor(track, highlight);
trackAlpha = generateTrackAlpha(track, highlight);
trackCurves.push({
xStart: xStart + 1,
yStart,
xEnd,
yEnd,
width: track.width,
color: trackColor,
alpha: trackAlpha,
laneChange: Math.abs(track.path[i].lane - track.path[i - 1].lane),
id: track.id,
name: track.name,
Expand Down Expand Up @@ -2921,6 +2942,7 @@ function generateSVGShapesFromPath() {
xEnd: Math.max(xStart, xEnd),
yEnd: yStart + track.width - 1,
color: trackColor,
alpha: trackAlpha,
id: track.id,
name: track.name,
type: track.type,
Expand Down Expand Up @@ -3333,13 +3355,15 @@ function colorNodes(nodeName) {
let nodesColors = {};
if (config.coloredNodes.includes(nodeName)) {
nodesColors["fill"] = "#ffc0cb";
nodesColors["fill-opacity"] = "0.4";
nodesColors["outline"] = "#ff0000";
} else {
nodesColors["fill"] = "#ffffff";
nodesColors["fill-opacity"] = "0.4";
nodesColors["outline"] = "#000000";
}
nodesColors["fill-opacity"] = "0.4";
if (config.transparentNodesFlag) {
nodesColors["fill"] = "none";
}
return nodesColors;
}

Expand Down Expand Up @@ -3809,6 +3833,7 @@ function drawTrackRectangles(rectangles, type, groupTrack) {
.attr("width", (d) => d.xEnd - d.xStart + 1)
.attr("height", (d) => d.yEnd - d.yStart + 1)
.style("fill", (d) => d.color)
.style("fill-opacity", (d) => d.alpha)
.attr("trackID", (d) => d.id)
.attr("trackName", (d) => d.name)
.attr("class", (d) => `track${d.id}`)
Expand Down Expand Up @@ -4110,6 +4135,7 @@ function drawTrackCurves(type, groupTrack) {
.append("path")
.attr("d", (d) => d.path)
.style("fill", (d) => d.color)
.style("fill-opacity", (d) => d.alpha)
.attr("trackID", (d) => d.id)
.attr("trackName", (d) => d.name)
.attr("class", (d) => `track${d.id}`)
Expand Down
Loading