genome-spy-python 0.8.0

v0.8.0

on Python PyPI

Added

• Optional Scanpy plotting integration through
  import genome_spy.integrations.scanpy as gsc, preserving supported plotting
  names and arguments while Scanpy continues to own analysis.
• Interactive embeddings, PCA diagnostics, dotplots, matrixplots, heatmaps,
  clustermaps, expression tracks, ranked-gene summaries, quality checks,
  time-series, DPT and PAGA plots. Unsupported plots and options fail explicitly.
• EmbeddingSummary for linked cell selections, expression summaries,
  histograms and marker tracks, with optional cell counts and selection retrieval
  in Python.
• Scanpy guides with live examples, downloadable notebooks, installation and
  export instructions, and documented coverage limits.

Changed

• Support Scanpy >=1.11.5,<1.13, tested with 1.11.5 and 1.12.4, while keeping
  the reference environment pinned independently.

Fixed

• Follow Scanpy 1.12's swapped-dotplot scaling and report its unavailable
  automatic PAGA tree layouts without substituting another layout.

Install

pip install --upgrade "genome-spy-python[scanpy]"

Scanpy docs and examples