print args in integration

KellisLab · Feb 26, 2024 · 46a57b5 · 46a57b5
1 parent 96dcf68
commit 46a57b5
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diff --git a/benj/integration.py b/benj/integration.py
@@ -233,7 +233,7 @@ def integrate_rna(adata, output=None, batch=None, hvg:int=0, use_combat:bool=Fal
         if len(dotplot) > 0:
             sc.pl.dotplot(adata, var_names=dotplot, groupby=leiden, save="%s.png" % leiden, standard_scale="var")
     for vv in np.intersect1d(["pct_counts_mt", "doublet_score", "log1p_total_counts"], adata.obs.columns):
-        sc.pl.violin(adata, vv, groupby=leiden, save="_%s_%s.png" % (leiden, vv))
+        sc.pl.violin(adata, vv, groupby=leiden, save="_%s_%s.png" % (leiden, vv), rotation=90)
     if use_rgg:
         from .rgg import extract_rank_genes_groups
         sc.tl.dendrogram(adata, groupby=leiden)

diff --git a/scripts/integrate_rna.py b/scripts/integrate_rna.py
@@ -35,5 +35,6 @@
     ap.add_argument("--no-save-data", dest="save_data", action="store_false")
     ap.set_defaults(use_combat=False, use_harmony=False, use_bbknn=True, use_scaling=False, use_rgg=True, save_data=False)
     args = benj.parse_args(ap, ["log", "scanpy", "anndata"])
+    print(args)
     adata = benj.parse_anndata(**args)
     benj.integrate_rna(adata, **args)