diff --git a/scripts/xenium_analysis_D216.py b/scripts/xenium_analysis_D216.py index 18a199125e37b918ee29a165b0d726397b5127cd..8846e939acfa4bb83409b73c82acd9171ecbb2b3 100644 --- a/scripts/xenium_analysis_D216.py +++ b/scripts/xenium_analysis_D216.py @@ -16,10 +16,10 @@ from spatialdata_io import xenium import sopa # Set parameters -xenium_data='/archive/urology/Strand_lab/shared/xenium/output-XETG00248__0034066__D216__20240425__175357/output-XETG00248__0034066__D216__20240425__175357' +xenium_data='/archive/urology/Strand_lab/shared/xenium/output-XETG00248__0034066__D216__20240425__175357' zarr_dir='data_modified/spatialdata_zarr/' sample_name='D216' -outdir='data_modified/xenium_D216/' +outdir='data_modified/xenium_'+sample_name+'/' os.makedirs(outdir, exist_ok=True) # Load data and create zarr store @@ -97,22 +97,23 @@ for i in res: ) # Create UMAP plots -umap_dir=outdir+'umaps/' -os.makedirs(umap_dir, exist_ok=True) -for i in res: - sc.pl.umap( - adata, - color='leiden_res_'+str(i), - save=umap_dir+'leiden_res_'+str(i)+'.png' - ) +grps=[ 'leiden_res_'+str(x) for x in res ] +sc.pl.umap( + adata, + color=grps, + ncols=3, + legend_loc='on data' +) +plt.savefig(fname=outdir+'umap_leiden.png') # Check gene expression genes=['EPCAM','KRT5','NKX3-1','PIGR','AKR1C2','DCN','ACTA2','DES','CDH19','PECAM1','PTPRC'] sc.pl.umap( adata, color=genes, - save=umap_dir+'lineage_markers.png' + ncols=3 ) +plt.savefig(fname=outdir+'umap_lineage_markers.png') # Save modified data adata.write_h5ad(outdir+sample_name+'_annotated.h5ad')