pirl-unc / tcrsift / 25868568643
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Close out #43: slope chart, n-methods distribution, signature scatter, (#64)

funnel variants, method-grouping helper

Ports the four remaining plots from the sarah-tcrseq-run2-run3 wrapper
into tcrsift.plots. After this, every plot family in #43 that has a
generic shape (not cohort-specific data) is upstreamed.

Ports:

- `plot_clone_tracking_slopes` — slope chart variant from
  `make_clone_tracking_plots.py:plot_slopes`. Per-source-sample panel,
  top-N clones' frequencies traced across every sample as connected
  lines. Source ordered first; remaining samples ordered by mean
  frequency over the source's top-N (decreasing). Log-y with the
  shared reference-fraction utility. (#43 item #1.)

- `plot_clones_by_n_methods` — 1-D distribution of clones × number of
  distinct samples present. Two side-by-side bars per bin: all
  surviving clones, plus tier-selected subset (tier1+tier2 by
  default) when a `tier` column is present. Symlog y-axis so
  singletons and highly-public clones both stay visible. Derives
  n-methods from an explicit `n_methods` column, falling back to
  `n_conditions_present`, then to counting non-zero entries in the
  per-clone `sample_frequencies` dict. (#43 item #6.)

- `plot_clone_freq_vs_signature_per_sample` — per-sample scatter of
  clone frequency vs. mean log1p expression of a gene set. Spearman
  correlation rendered as a corner annotation. Default gene-set
  constants `ACTIVATION_GENES_HGNC = (IFNG, GZMB, PRF1, GNLY, NKG7)`
  and `EXHAUSTION_GENES_HGNC = (PDCD1, LAG3, HAVCR2, TIGIT, TOX,
  CTLA4)` pulled from the wrapper's published cohort work; callers
  override via the `gene_ids` argument. Gracefully skips when the
  gene list has zero overlap with `adata.var_names` or when the
  adata is missing the `sample` / `CDR3ab` obs columns. (#43 item
  #7.)

- Funnel variants — three new siblings to the existing `plot_funnel`
  bars renderer:
  * `plot_funnel_ribbon` — smooth narrowing polygon, inner tick
    marks preserve ... (continued)

5413 of 7327 relevant lines covered (73.88%)

2.95 hits per line

Coverage Regressions

Lines Coverage ∆ File
207
55.28
 17.0% plots.py
Jobs
ID Job ID Ran Files Coverage
1 python-3.12 - 25868568643.1 25
73.87
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2 python-3.10 - 25868568643.2 25
73.87
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3 python-3.9 - 25868568643.3 25
73.85
 GitHub Action Run
4 python-3.11 - 25868568643.4 25
73.87
 GitHub Action Run
Source Files on build 25868568643