From 25bf649f8766fe00dec83ea3c0183de28de5514d Mon Sep 17 00:00:00 2001 From: Jean Monlong Date: Wed, 28 Aug 2024 20:34:07 +0200 Subject: [PATCH 01/11] make nodes fully transparent again --- src/util/tubemap.js | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/util/tubemap.js b/src/util/tubemap.js index 471d041f..030eef24 100644 --- a/src/util/tubemap.js +++ b/src/util/tubemap.js @@ -3333,13 +3333,15 @@ 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; } From 90cb8d4f82fe1edafe838f71ffe533e290f81352 Mon Sep 17 00:00:00 2001 From: Jean Monlong Date: Wed, 28 Aug 2024 20:34:57 +0200 Subject: [PATCH 02/11] add a checkbox to have read transparency by mapq --- src/App.js | 1 + src/components/CustomizationAccordion.js | 12 +++++++++++ src/components/HeaderForm.js | 4 +++- src/components/TrackList.demo.js | 3 +++ src/components/TrackList.test.js | 3 +++ src/components/TrackListItem.demo.js | 1 + src/components/TrackListItem.test.js | 1 + src/components/TrackPickerDisplay.demo.js | 3 +++ src/components/TrackPickerDisplay.test.js | 1 + src/components/TrackSettings.demo.js | 1 + src/components/TrackSettings.js | 4 +++- src/components/TrackSettings.test.js | 1 + src/components/TrackSettingsButton.demo.js | 1 + src/components/TrackSettingsButton.test.js | 1 + src/components/TubeMap.js | 1 + src/util/tubemap.js | 24 ++++++++++++++++++++++ 16 files changed, 60 insertions(+), 2 deletions(-) diff --git a/src/App.js b/src/App.js index 271741fd..24d25228 100644 --- a/src/App.js +++ b/src/App.js @@ -65,6 +65,7 @@ class App extends Component { showReads: true, showSoftClips: true, colorReadsByMappingQuality: false, + alphaReadsByMappingQuality: false, colorSchemes: getColorSchemesFromTracks(this.defaultViewTarget.tracks), mappingQualityCutoff: 0, }, diff --git a/src/components/CustomizationAccordion.js b/src/components/CustomizationAccordion.js index 22219024..6aea8e0c 100644 --- a/src/components/CustomizationAccordion.js +++ b/src/components/CustomizationAccordion.js @@ -197,6 +197,18 @@ class VisualizationOptions extends Component { Color reads by mapping quality + + +