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PCA / t-SNE: colour by sample type, plate or study group - #57
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Issue #48 item 5. Both projections get a "Colour by" dropdown with the colourings that separate samples: sample type (or QC flag), plate when there are several, and the study group when the SDRF or sample metadata defines one (SDRF factor values named as such; controls and unannotated samples in grey). Works in the full and the split report. PAD000040: PC1 separates the two plates while the glycemic groups mix, showing the plate effect directly.
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Closes #48 (items 1–3 in #56, item 4 answered on the issue).
Item 5 of #48. Stacked on #56 (stack: #52 → #53 → #55 → #56 → this).
PCA and t-SNE get a "Colour by" dropdown, listing only colourings that separate the samples:
factor value[...]; control samples and unannotated samples are grey.It works in both the full report and the split pages PRIDE embeds, and the "Show Labels" button still works.
This helps QC, not only interpretation: it shows whether the main structure follows plate, sample type or biology. On PAD000040, PC1 separates the two plates while the three glycemic groups are mixed, which shows directly that the plates aren't bridge-normalised. Study groups appear only when the SDRF declares them (6 public datasets today).
The correlation and expression heatmaps are unchanged. A group annotation strip there is more work and less readable; it can follow if wanted.
Tests