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ADD cau-qc: the quality-control pass over an assembled channel - #20

Merged

emattei merged 31 commits into

mainfrom

feat/qc-figures

Nov 9, 2026

Merged

ADD cau-qc: the quality-control pass over an assembled channel#20
emattei merged 31 commits into
mainfrom
feat/qc-figures

Commits on Oct 15, 2026
- ADD the qc module: figures that publish their own numbers
  
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  b4f927f
- UPDATE mad_outlier to a sigma-scaled MAD on log10
  
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  0a659b6
- FIX the skill's account of why the MAD needs cells first
  
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  fff86b6
- ADD metric_distributions, one histogram per QC metric
  
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  91f35d5
- FIX the log bins starting at 1 rather than at the data
  
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- UPDATE the distribution colours: blue kept, grey removed
  
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  1f4e163
- FIX cells on the outermost value going uncounted
  
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  5bd9434
- FIX the flagged layer painting over the kept cells
  
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  fc363fb
- REWRITE metric_distributions to split at each metric's threshold
  
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  50aaef6
- ADD metric_scatter, two QC metrics against each other
  
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  cb1b6a2
- UPDATE the scatter to drop its legend when nothing is removed
  
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  9440132
- ADD extra gene classes to cell_fractions
  
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  578fca6
- ADD panel_expression and mean_upm
  
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  c13d850
- FIX the panel caption reading "a inf-fold difference"
  
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  e1dedf6
- ADD a unit to metric_scatter so it serves a per-gene comparison
  
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  b02b4b7
- FIX a zero vanishing from a log-axis scatter without saying so
  
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  da685e5
- UPDATE the scatter's points to follow how many there are
  
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  bc56065
- FIX the adaptive point size the previous commit only tested
  
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  b965e5a
- ADD groups to metric_scatter, colouring by label not by threshold
  
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  be7f41a
- FIX group colours depending on the order the rows arrived in
  
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  a046717
- UPDATE grouped points to draw solid over a see-through background
  
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  5201bb1
- ADD a thin dark outline to the labelled points
  
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  92ebe74
- UPDATE the distribution panels to say what their lines cut
  
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  05720ce
- FIX the line labels, which sat outside the band and were cut off
  
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  d22e79b
- FIX the caption, which counted cells and called them bars
  
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  a76b231
- FIX the log tick labels, which overlapped on a narrow span
  
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  c1dc6a4
- ADD the filtering step and the filtered object it writes
  
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  27d4dc8
- ADD band, to measure a band for only some of the metrics
  
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  f5b8b03
- UPDATE the panels to draw the rules the file is cut on
  
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  029f3e2
- ADD the guide counts and the guides a channel never saw
  
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  6809bb5
Commits on Nov 9, 2026
- MERGE main into the QC figures branch
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  506a3f5

Commits

Commits on Oct 15, 2026

Commits on Nov 9, 2026