scanpy 绘制marker基因点图
scanpy 绘制marker基因点图
Rscript $scripts/seuratObj2anndata.r -i ../03.seurat_cluster/pbmc.qs -p harmony_seurat_clusters --assay RNA --layer data
python3 $scripts/scanpy_dotplot.py -i harmony_seurat_clusters.h5ad --layer data \
--groupby seurat_clusters -p Marker.seurat_clusters -W 15 -H 6 --color_map viridis --standard_scale var \
--var_names '{
"CD14+ Mono": ["CD14", "LYZ"],
"CD4+ Naive T": ["CCR7","SELL"],
"CD4+ Memory T": [ "IL7R","CD27"],
"CD8+ T": ["CD8A"],
"B": ["MS4A1"],
"NK": ["GNLY", "NKG7"],
"FCGR3A+ Mono": ["FCGR3A", "MS4A7"],
"T activated": ["CREM", "CD69"],
"mDC": ["FCER1A", "CST3"],
"Platelet": ["PPBP"],
"pDC": ["LILRA4", "IRF7", "TLR7"],
"Erythrocyte": ["HBB", "HBA2"]
}'
- 发表于 6天前
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- 分类：转录组
