From a3e90cde84d125d66f47f0d7906d1adfc87d7c5e Mon Sep 17 00:00:00 2001 From: Adam Wright Date: Fri, 30 Oct 2026 18:44:55 +0000 Subject: [PATCH 1/4] Explain DeltaSignal's result columns in the panel MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit A curator could not tell what Influence, or the other columns, meant. The table's headers now say what each number is (activity × normal, change vs baseline), and a short "What do these columns mean?" note, opened in place, defines each column in plain words from DeltaSignal's own API documentation, and says how the rows are sorted and grouped. Co-Authored-By: Claude Opus 5.5 --- .../deltasignal-panel.component.html | 31 +++++++++++++++++- .../deltasignal-panel.component.scss | 32 +++++++++++++++++++ 2 files changed, 62 insertions(+), 1 deletion(-) diff --git a/projects/pathway-browser/src/app/deltasignal/deltasignal-panel.component.html b/projects/pathway-browser/src/app/deltasignal/deltasignal-panel.component.html index 06fd12793..ffd772e2c 100644 --- a/projects/pathway-browser/src/app/deltasignal/deltasignal-panel.component.html +++ b/projects/pathway-browser/src/app/deltasignal/deltasignal-panel.component.html @@ -206,9 +206,38 @@

Predicted response

entity, all values appear as a gradient. The pathway diagram remains interactive beside this panel.

+
+ What do these columns mean? +
+
Activity
+
+ The entity's predicted activity once the network settles, on the same scale as the input: 1× is normal, + 0 is none, and higher is more active. +
+
Change
+
+ Predicted activity minus the entity's own normal (baseline) activity: below zero it falls, above zero it + rises. The diagram's colours show this. +
+
Influence
+
+ How strongly the reactions this entity takes part in respond to a small change in it, at the predicted + state. Higher means it matters more to the result; it is a ranking, not a unit. +
+
+

+ Rows are sorted by the size of the change; a highlighted row is one you perturbed. Where one entity is + several nodes of the logic network, its row shows their average activity and change and their largest + influence. +

+
+
- EntityActivityChangeInfluence + Entity + Activity (× normal) + Change vs baseline + Influence
@for (row of visibleRows(); track row.uuid) {
diff --git a/projects/pathway-browser/src/app/deltasignal/deltasignal-panel.component.scss b/projects/pathway-browser/src/app/deltasignal/deltasignal-panel.component.scss index b6f712cf8..bd5d1a7e8 100644 --- a/projects/pathway-browser/src/app/deltasignal/deltasignal-panel.component.scss +++ b/projects/pathway-browser/src/app/deltasignal/deltasignal-panel.component.scss @@ -329,6 +329,38 @@ main { font: var(--mat-sys-body-small); } +.column-help { + margin: 0 0 12px; + color: var(--on-surface-variant); + font: var(--mat-sys-body-small); + + summary { + cursor: pointer; + color: var(--primary); + font: var(--mat-sys-label-large); + } + + dl { + display: grid; + grid-template-columns: max-content 1fr; + gap: 6px 12px; + margin: 10px 0 6px; + } + + dt { + color: var(--on-surface); + font-weight: 500; + } + + dd { + margin: 0; + } + + p { + margin: 0; + } +} + .result-table { max-height: 360px; overflow: auto; From a214cb5372fa117c03c1cc932c4c83528aa36fb2 Mon Sep 17 00:00:00 2001 From: Adam Wright Date: Fri, 30 Oct 2026 18:48:08 +0000 Subject: [PATCH 2/4] DeltaSignal's columns, from #765's review: Influence as it is computed MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Influence counts only the reactions an entity feeds (substrate, catalyst, activator, inhibitor), at the predicted state: a direct, local effect, not its effect on the whole pathway; one that feeds no reaction scores 0. Change is a difference on the × scale, so a fall reaches -1 and a rise +99, and large rises sort above every fall. Data cells get role="cell" beside the headers' columnheader. Co-Authored-By: Claude Opus 5.5 --- .../deltasignal-panel.component.html | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/projects/pathway-browser/src/app/deltasignal/deltasignal-panel.component.html b/projects/pathway-browser/src/app/deltasignal/deltasignal-panel.component.html index ffd772e2c..791fa0b8c 100644 --- a/projects/pathway-browser/src/app/deltasignal/deltasignal-panel.component.html +++ b/projects/pathway-browser/src/app/deltasignal/deltasignal-panel.component.html @@ -216,13 +216,15 @@

Predicted response

Change
- Predicted activity minus the entity's own normal (baseline) activity: below zero it falls, above zero it - rises. The diagram's colours show this. + Predicted activity minus the entity's own normal (baseline) activity, on the same scale: below zero it + falls, above zero it rises. A fall can reach −1 (switched off); a rise can reach +99, so large rises + sort above every fall. The diagram's colours show this.
Influence
- How strongly the reactions this entity takes part in respond to a small change in it, at the predicted - state. Higher means it matters more to the result; it is a ranking, not a unit. + How strongly the reactions this entity feeds (as a substrate, catalyst, activator or inhibitor) respond + to a small change in it, at the predicted state. It ranks the entity's direct, local effect, not its + effect on the whole pathway, and has no unit; an entity that feeds no reaction scores 0.

@@ -241,15 +243,15 @@

Predicted response

@for (row of visibleRows(); track row.uuid) {
- + {{ row.name }} {{ row.reactomeId }} - {{ row.activity | number: '1.1-1' }}× - + {{ row.activity | number: '1.1-1' }}× + {{ row.change > 0 ? '+' : '' }}{{ row.change | number: '1.1-1' }} - {{ row.influence | number: '1.2-2' }} + {{ row.influence | number: '1.2-2' }}
}
From 554b1498ff83974b4125c9cc9b0af4b604a934bd Mon Sep 17 00:00:00 2001 From: Adam Wright Date: Fri, 30 Oct 2026 18:52:04 +0000 Subject: [PATCH 3/4] DeltaSignal's columns, from #766's review: Influence over everything an entity feeds MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The listed roles missed paths DeltaSignal counts: a reaction's products, a set's pool, a catalyst's depleted substrate. Influence is now described as the response of everything the entity feeds directly in the logic network, which the "Logic nodes & edges" view shows. The Activity header drops "(× normal)", which every cell already shows. Co-Authored-By: Claude Opus 5.5 --- .../src/app/deltasignal/deltasignal-panel.component.html | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/projects/pathway-browser/src/app/deltasignal/deltasignal-panel.component.html b/projects/pathway-browser/src/app/deltasignal/deltasignal-panel.component.html index 791fa0b8c..968c55cae 100644 --- a/projects/pathway-browser/src/app/deltasignal/deltasignal-panel.component.html +++ b/projects/pathway-browser/src/app/deltasignal/deltasignal-panel.component.html @@ -222,9 +222,10 @@

Predicted response

Influence
- How strongly the reactions this entity feeds (as a substrate, catalyst, activator or inhibitor) respond - to a small change in it, at the predicted state. It ranks the entity's direct, local effect, not its - effect on the whole pathway, and has no unit; an entity that feeds no reaction scores 0. + How strongly everything this entity feeds directly in the logic network (the reactions it takes in, + catalyses or regulates, a set it belongs to, and so on; the “Logic nodes & edges” view shows these + links) responds to a small change in it, at the predicted state. It ranks direct, local effect, not + effect on the whole pathway, and has no unit; an entity that feeds nothing scores 0.

@@ -237,7 +238,7 @@

Predicted response

Entity - Activity (× normal) + Activity Change vs baseline Influence
From a7040cbf6333a440cc1f6cc18e821df25bf99609 Mon Sep 17 00:00:00 2001 From: Adam Wright Date: Fri, 30 Oct 2026 18:52:19 +0000 Subject: [PATCH 4/4] Influence's wording: the reactions it is an input to Co-Authored-By: Claude Opus 5.5 --- .../src/app/deltasignal/deltasignal-panel.component.html | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/projects/pathway-browser/src/app/deltasignal/deltasignal-panel.component.html b/projects/pathway-browser/src/app/deltasignal/deltasignal-panel.component.html index 968c55cae..5c22174b2 100644 --- a/projects/pathway-browser/src/app/deltasignal/deltasignal-panel.component.html +++ b/projects/pathway-browser/src/app/deltasignal/deltasignal-panel.component.html @@ -222,10 +222,10 @@

Predicted response

Influence
- How strongly everything this entity feeds directly in the logic network (the reactions it takes in, - catalyses or regulates, a set it belongs to, and so on; the “Logic nodes & edges” view shows these - links) responds to a small change in it, at the predicted state. It ranks direct, local effect, not - effect on the whole pathway, and has no unit; an entity that feeds nothing scores 0. + How strongly everything this entity feeds directly in the logic network (the reactions it is an input + to, catalyses or regulates, a set it belongs to, and so on; the “Logic nodes & edges” view shows + these links) responds to a small change in it, at the predicted state. It ranks direct, local effect, + not effect on the whole pathway, and has no unit; an entity that feeds nothing scores 0.