66 lines
2.2 KiB
Python
66 lines
2.2 KiB
Python
#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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"""
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04c_marker_dotplot_full.py — 用完整官方表 S3 marker 列表重画注释证据 dotplot
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S3 全量 32 基因 + 我们补充的 marker（S3 未覆盖的细胞类型用 "***" 分组标注）
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产出：output/04_annotation/marker_dotplot_fullS3.png
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"""
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from pathlib import Path
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import matplotlib
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matplotlib.use("Agg")
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import matplotlib.pyplot as plt
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import scanpy as sc
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OUT = Path("output/04_annotation")
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plt.rcParams.update({"figure.dpi": 300, "savefig.dpi": 300, "font.size": 8})
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# 官方表 S3 全量
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S3 = {
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"Rod": ["Cnga1", "Cngb1", "Gnat1", "Rho", "Rp1", "Sag", "Ush2a"],
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"Cone": ["Arr3", "Cngb3", "Gnat2", "Opn1mw"],
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"RGC": ["Rbpms", "Slc17a6", "Thy1"],
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"Amacrine": ["Gad1", "Gad2", "Grm5", "Slc6a5", "Tfap2b"],
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"Muller": ["Rlbp1", "Slc1a3"],
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"Uveal": ["Gpnmb", "Tyr"],
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"Bipolar": ["Cabp5", "Grm6", "Kcnb2", "Prkca"],
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"Horizontal": ["Lhx1", "Onecut2", "Prox1"],
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"Pericyte": ["Pdgfrb", "Rgs5"],
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}
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# 本项目补充（S3 未覆盖的细胞类型/补充基因）
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EXTRA = {
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"Muller+": ["Glul"],
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"Bipolar+": ["Vsx2"],
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"Microglia*": ["Aif1", "C1qa", "C1qb", "Tmem119", "Hexb"],
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"Astrocyte*": ["Gfap", "S100b", "Aqp4"],
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"Endothelial*": ["Pecam1", "Cldn5", "Kdr"],
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"Oligodendrocyte*": ["Mog", "Plp1", "Mbp"],
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}
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adata = sc.read_h5ad("data/03_annotated.h5ad")
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var = set(adata.raw.var_names)
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panel = {}
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for src in (S3, EXTRA):
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for ct, gs in src.items():
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ok = [g for g in gs if g in var]
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missing = set(gs) - set(ok)
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if missing:
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print(f"[警告] {ct} 缺失: {missing}")
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panel[ct] = ok
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# 按注释细胞类型排序 cluster
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order = (
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adata.obs.groupby("leiden_0.8", observed=True)["cell_type"]
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.agg(lambda x: x.mode()[0])
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.sort_values()
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)
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adata.obs["ct_cluster"] = adata.obs["cell_type"].astype(str) + " | c" + adata.obs["leiden_0.8"].astype(str)
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ct_order = sorted(adata.obs["ct_cluster"].unique(), key=lambda s: (s.split(" | ")[0], int(s.split(" | c")[1])))
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fig = sc.pl.dotplot(
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adata, var_names=panel, groupby="ct_cluster", categories_order=ct_order,
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use_raw=True, show=False, return_fig=True,
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)
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fig.savefig(OUT / "marker_dotplot_fullS3.png", bbox_inches="tight")
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print("Done ->", OUT / "marker_dotplot_fullS3.png")
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