Add group percentages to oncoprint #4756
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Collaborator
alisman
commented
Oct 17, 2023
•
alisman
commented
- Show group percentages in Oncoprint when gaps are turned on
- Show labels in SVG download
- Should also work in Oncoprinter
- Should work in merged tracks
alisman
force-pushed
the
onco-groups
branch
2 times, most recently
from
7472799 to
507542a
Compare
onursumer
reviewed
Nov 2, 2023
Comment on lines
2093
to
2095
| // aaron | ||
| // aaron |
There was a problem hiding this comment.
we should remove/replace these comments
Comment on lines
643
to
649
| const percentagesForGroups = groupsByTrackMap[gene][0].map( | ||
| groupData => { | ||
| return getPercentAltered( | ||
| groupData as OncoprinterGeneticTrackDatum[] | ||
| ); | ||
| } | ||
| ); |
There was a problem hiding this comment.
would be simpler if we could do something like
Suggested change
| const percentagesForGroups = groupsByTrackMap[gene][0].map( | |
| groupData => { | |
| return getPercentAltered( | |
| groupData as OncoprinterGeneticTrackDatum[] | |
| ); | |
| } | |
| ); | |
| const percentagesForGroups = groupsByTrackMap[gene][0].map(getPercentAltered); |
Comment on lines
+849
to
+876
| sequencedPatientKeysForGroup = _( | ||
| geneSymbolArray | ||
| ) | ||
| .keyBy(gene => gene) | ||
| .mapValues(gene => { | ||
| // you want to return only the patient ids which are listed as | ||
| // sequenced for the gene(s) in this track (plural in case of merged tracks) | ||
| return _.intersection( | ||
| _.flatMap( | ||
| geneSymbolArray, | ||
| gene => | ||
| sequencedPatientKeysByGene[ | ||
| gene | ||
| ] | ||
| ), | ||
| groupData.map((d: any) => d.uid) | ||
| ); | ||
| }) | ||
| .value(); |
There was a problem hiding this comment.
this else block is almost identical to the if block above except the variables sequencedSampleKeysByGene vs sequencedPatientKeysByGene. probably better to extract the logic to a function and reuse.
Comment on lines
+315
to
+347
| const overlappingGap = self.gapTooltipTargets.find( | ||
| (t: any) => { | ||
| return ( | ||
| _.inRange(mouseX - t.origin_x, 0, 20) && | ||
| _.inRange(t.origin_y - mouseY, -10, 15) | ||
| ); | ||
| } | ||
| ); | ||
|
|
||
| // if there is no gap, turn | ||
| if (overlappingGap === undefined) { | ||
| self.hoveredGap = undefined; | ||
| } else if (self.hoveredGap === overlappingGap) { | ||
| // tooltip should already be showing, so do nothing | ||
| } else { | ||
| // we have a new hovered gap, so show a tooltip | ||
| const clientRect = self.$overlay_canvas[0].getBoundingClientRect(); | ||
| self.hoveredGap = overlappingGap; | ||
| tooltip.center = false; | ||
| tooltip.show( | ||
| 250, | ||
| clientRect.left + overlappingGap.origin_x, | ||
| clientRect.top + overlappingGap.origin_y - 20, | ||
| $( | ||
| `<span>${overlappingGap.data.tooltipFormatter()}</span>` | ||
| ), | ||
| false | ||
| ); | ||
| } | ||
|
|
||
| if (!overlapping_data && !overlappingGap) { | ||
| tooltip.hideIfNotAlreadyGoingTo(150); | ||
| } |
There was a problem hiding this comment.
so much work to show a tooltip but I guess we have no other choice 😞
There was a problem hiding this comment.
@onursumer I think It's been said the hardest problems in computer science are 1) knowing when to clear a cache and 2) making a tooltip over an HTML canvas.
Comment on lines
434
to
444
| //ctx.clearColor(1.0, 1.0, 1.0, 1.0); | ||
| //ctx.clear(ctx.COLOR_BUFFER_BIT | ctx.DEPTH_BUFFER_BIT); | ||
| // ctx.viewportWidth = canvas.width; | ||
| // ctx.viewportHeight = canvas.height; | ||
| // ctx.viewport(0, 0, ctx.viewportWidth, ctx.viewportHeight); | ||
| //ctx.enable(ctx.DEPTH_TEST); | ||
| //ctx.enable(ctx.BLEND); | ||
| //ctx.blendEquation(ctx.FUNC_ADD); | ||
| //ctx.blendFunc(ctx.SRC_ALPHA, ctx.ONE_MINUS_SRC_ALPHA); | ||
| //ctx.depthMask(false); |
There was a problem hiding this comment.
should we remove this or add a comment why we commented it out?
Comment on lines
634
to
644
| //ctx.clearColor(1.0, 1.0, 1.0, 1.0); | ||
| //ctx.clear(ctx.COLOR_BUFFER_BIT | ctx.DEPTH_BUFFER_BIT); | ||
| //ctx. = canvas.width; | ||
| //ctx.viewportHeight = canvas.height; | ||
| //ctx.viewport(0, 0, ctx.viewportWidth, ctx.viewportHeight); | ||
| //ctx.enable(ctx.DEPTH_TEST); | ||
| //ctx.enable(ctx.BLEND); | ||
| //ctx.blendEquation(ctx.FUNC_ADD); | ||
| //ctx.blendFunc(ctx.SRC_ALPHA, ctx.ONE_MINUS_SRC_ALPHA); | ||
| //ctx.depthMask(false); |
There was a problem hiding this comment.
same as above, except here we have a syntax error ctx. = canvas.width; :)
Comment on lines
+2071
to
+2037
| const gaps = _.isEmpty(model.ids_after_a_gap.get()) | ||
| ? undefined | ||
| : custom.find(t => !!t.gapLabelsFn)?.gapLabelsFn(model); |
There was a problem hiding this comment.
duplicate code segment. should we define a getGaps function? we can probably include this one as well const custom = model.getTrackCustomOptions(track_id);
alisman
force-pushed
the
onco-groups
branch
6 times, most recently
from
55adeb6 to
1e2ff1d
Compare
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.