From d80269a8a17da82d71fce78f2f53cb54f968d119 Mon Sep 17 00:00:00 2001 From: Benjamin James Date: Thu, 25 Jan 2024 17:14:12 -0500 Subject: [PATCH] Only dotplot genes in var_names --- benj/integration.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/benj/integration.py b/benj/integration.py index 13fbae4..761e68c 100644 --- a/benj/integration.py +++ b/benj/integration.py @@ -229,7 +229,7 @@ def integrate_rna(adata, output=None, batch=None, hvg:int=0, use_combat:bool=Fal sc.pl.umap(adata, color=leiden, save="_%s_ondata.png" % leiden, legend_loc="on data", legend_fontsize=2) if dotplot is not None: if not isinstance(dotplot, str): - dotplot = np.ravel([x.split(",") for x in dotplot]) + dotplot = np.intersect1d(np.ravel([x.split(",") for x in dotplot]), adata.var_names) 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))