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Reimplement the tree / network #15

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merged 29 commits into from
Sep 9, 2022
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cfb743d
First pass at reimplementing deterministically with equal angle algo
sidneymbell Aug 30, 2022
b9f776b
Merge branch 'add-logo-subtitle' into large-clade-forcegraph-fix
sidneymbell Aug 30, 2022
81e4b6c
Merge branch 'main' into large-clade-forcegraph-fix
sidneymbell Aug 30, 2022
c4f4a9c
Fix logo positioning (one-off)
sidneymbell Aug 30, 2022
2cc1baf
Merge branch 'main' into large-clade-forcegraph-fix
sidneymbell Sep 2, 2022
5976fa3
Fix tip count traversal (swear words)
sidneymbell Sep 2, 2022
c017879
be a bit more generous in the way we look for division and location
sidneymbell Sep 2, 2022
8738c5c
update package lock
sidneymbell Sep 2, 2022
2c8d92e
Attempt 2
sidneymbell Sep 2, 2022
e4b7c74
cruft cleanup
sidneymbell Sep 2, 2022
d8ef189
fix the damn bug
sidneymbell Sep 2, 2022
6fa3fad
cleanup
sidneymbell Sep 3, 2022
3a33d8f
restore coloring, draw links underneath
sidneymbell Sep 3, 2022
3509313
Handle polytomies
sidneymbell Sep 7, 2022
d5a5f92
Readability
sidneymbell Sep 7, 2022
435ec9a
Move aux functions to utils where possible
sidneymbell Sep 7, 2022
a28fd5b
Default value
sidneymbell Sep 7, 2022
a517334
Fix demo muts per transmission value
sidneymbell Sep 7, 2022
89a3734
Version with mrca square, SoI marker, tooltips
sidneymbell Sep 7, 2022
85281a6
comments and readability
sidneymbell Sep 7, 2022
ff465fa
rename
sidneymbell Sep 7, 2022
c919455
squares as (containing) samples of interest
sidneymbell Sep 7, 2022
811efcc
fix tooltip
sidneymbell Sep 7, 2022
dfe98f1
cleanup for readability
sidneymbell Sep 7, 2022
de134f6
Massive prettier / lint commit (!?)
sidneymbell Sep 7, 2022
e06365a
Merge branch 'main' into large-clade-forcegraph-fix
sidneymbell Sep 7, 2022
391dfd0
Cleanup defunct files
sidneymbell Sep 7, 2022
cf4aa6a
One more defunct file
sidneymbell Sep 7, 2022
43872e1
Merge remote-tracking branch 'labs-origin/main' into large-clade-forc…
sidneymbell Sep 8, 2022
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23,427 changes: 21,516 additions & 1,911 deletions package-lock.json

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1 change: 1 addition & 0 deletions package.json
Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@
"@redux-devtools/extension": "^3.2.2",
"@visx/axis": "^2.6.0",
"@visx/heatmap": "^2.10.0",
"@visx/tooltip": "^2.10.0",
"@visx/visx": "^2.10.0",
"axios": "^0.27.2",
"d3": "^7.4.0",
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4 changes: 2 additions & 2 deletions src/components/header.tsx
Original file line number Diff line number Diff line change
Expand Up @@ -66,8 +66,8 @@ const Header = (props: HeaderProps) => {
<div
style={{
position: "absolute",
left: 20,
top: 20,
left: 0,
top: 0,
fontSize: 24,
margin: 0,
}}
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3 changes: 2 additions & 1 deletion src/components/mainViz.tsx
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ import { useDispatch } from "react-redux";
import { ForceGraph } from "./viz/drawForceGraph";
import ToggleButtonGroup from "@mui/material/ToggleButtonGroup/ToggleButtonGroup";
import ToggleButton from "@mui/material/ToggleButton";
import UnrootedTree from "./viz/unrootedTree";

type MainVizProps = {
sectionHeight: number;
Expand Down Expand Up @@ -46,7 +47,7 @@ export const MainViz = (props: MainVizProps) => {
}}
>
{viewPlot === "forceGraph" && state.mrca ? (
<ForceGraph
<UnrootedTree
chartWidth={chartWidth}
chartHeight={chartHeight}
chartMargin={chartMargin}
Expand Down
155 changes: 0 additions & 155 deletions src/components/viz/drawForceGraph/drawForceLink.tsx

This file was deleted.

34 changes: 0 additions & 34 deletions src/components/viz/drawForceGraph/drawLabels.tsx

This file was deleted.

153 changes: 0 additions & 153 deletions src/components/viz/drawForceGraph/drawNodes.tsx

This file was deleted.

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