eugenegujing opened a new issue, #9039: URL: https://github.com/apache/texera/issues/9039
### Feature Summary The Volcano Plot operator (`common/workflow-operator/src/main/scala/org/apache/texera/amber/operator/visualization/volcanoPlot/VolcanoPlotOpDesc.scala`) renders a plain `px.scatter` of effect vs `-log10(p)` with `color=$effectColumn, color_continuous_scale="RdBu"` (`:113-121`). Two things are missing that make it a volcano plot rather than a scatter plot: 1. No threshold lines. Readers expect a horizontal line at the significance cut-off (e.g. padj = 0.05 → y = 1.30) and vertical lines at ±effect cut-off (e.g. |log2FC| = 1). Without them you cannot read from the figure whether anything is significant. In our DE run every padj was ≈ 0.999, so the whole plot sat between y = 0.00007 and y = 0.00028, and nothing on the figure showed that y = 1.3 was the bar to clear. 2. Color carries no information. The point color is the effect-size value, which is already the x coordinate. The usual convention in volcano-plot tooling (EnhancedVolcano, ggvolc, bullkpy) is categorical: points that pass both cut-offs are colored by direction (up / down) and everything else is muted. ### Proposed Solution or Design Three optional properties, all off by default so saved workflows render as today: a significance threshold (dashed horizontal line at `-log10` of it), an effect-size threshold (dashed vertical lines at ± it), and a "Color by significance" toggle that, when both thresholds are set, colors points Up (p below the cut-off and effect above +threshold), Down (p below the cut-off and effect below −threshold) or Not significant, with a legend, instead of the continuous scale. Both thresholds apply to whichever p-value column the user selected. ### Affected Area _No response_ -- This is an automated message from the Apache Git Service. To respond to the message, please log on to GitHub and use the URL above to go to the specific comment. To unsubscribe, e-mail: [email protected] For queries about this service, please contact Infrastructure at: [email protected]
