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Volcano Plot labels the y axis "-log10(pvalue)" regardless of the selected column, and offers no title / axis / color-bar labels #9037
Description
What happened?
VolcanoPlotOpDesc.generatePythonCode (common/workflow-operator/src/main/scala/org/apache/texera/amber/operator/visualization/volcanoPlot/VolcanoPlotOpDesc.scala:111-120) hard-codes every text element of the figure:
table["-log10(pvalue)"] = -np.log10(table[$pvalueColumn]) # :111
fig = px.scatter(
table,
x=$effectColumn,
y="-log10(pvalue)", # :116 y-axis title
hover_name=table.columns[0],
color=$effectColumn, # color bar title = raw column name
color_continuous_scale="RdBu",
title="Volcano Plot" # :120
)The property panel exposes only Effect Size (log2 Fold Change) and P-Value Column. Whatever column is selected as the p-value input, the y axis is titled -log10(pvalue).
In practice the p-value input is almost always a multiple-testing-adjusted value (DESeq2 padj, limma adj.P.Val, BH / Storey q-values). With pvalueColumn = padj the figure says -log10(pvalue), i.e. it tells the reader the y axis is the raw p-value. Nobody can tell the difference from the figure, and there is no title, x-label, y-label or color-bar-label property to fix it from the UI. The x axis and color bar show the raw column name (lfc_shrunk, delta_pdui), which is not a publication label either.
Concrete case (RNA-seq differential expression + differential APA, two volcano plots in one workflow):
| Figure | Column chosen | What the figure should say | What Texera renders |
|---|---|---|---|
| DE volcano, y | padj |
−log₁₀(BH-adjusted p-value) | -log10(pvalue) |
| DE volcano, x | lfc_shrunk |
Shrunken log₂ fold change (NAS1 / NAS0) | lfc_shrunk |
| DE volcano, color bar | lfc_shrunk |
Shrunken log₂ fold change | lfc_shrunk |
| APA volcano, y | padj |
−log₁₀(BH-adjusted p-value) | -log10(pvalue) |
| APA volcano, x | delta_pdui |
ΔPDUI (NAS1 − NAS0) | delta_pdui |
The APA case also shows that the fixed log2 Fold Change wording in the property title (:47) is too narrow: that effect column is a difference of proportions, not a log fold change. We had to send collaborators a separate note explaining that the y label on both plots is wrong and what the axes actually mean.
Expected: the y-axis title names the column that was actually transformed (e.g. -log10(padj)), and the title / axis / color-bar text can be set from the property panel, as Line Chart already allows for its axes.
How to reproduce?
- Any source whose rows have a numeric effect column and a numeric adjusted-p column, e.g. a CSV with
gene,lfc_shrunk,padj. - Volcano Plot → Effect Size =
lfc_shrunk, P-Value Column =padj. - Run; open the result.
Version/Branch
1.4.0-incubating-SNAPSHOT (main)
Commit Hash (Optional)
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What browsers are you seeing the problem on?
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