From 05efba0570b056622f0636ebcadd13ae0b75d012 Mon Sep 17 00:00:00 2001
From: John Lafin <john.lafin@utsouthwestern.edu>
Date: Tue, 18 Feb 2025 15:58:57 -0600
Subject: [PATCH] Update Xe D216 script to match others
---
scripts/xenium_analysis_D216.py | 23 ++++++++++++-----------
1 file changed, 12 insertions(+), 11 deletions(-)
diff --git a/scripts/xenium_analysis_D216.py b/scripts/xenium_analysis_D216.py
index 18a1991..8846e93 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')
--
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