Merge pull request #184 from zhanghao-njmu/develop

Develop

inst/python/SCP_analysis.py

@@ -278,16 +278,15 @@ def SCVELO(adata=None, h5ad=None, group_by=None, palette=None,
             adata.uns["rank_"+vkey+"_genescores"]=df2
             del adata.uns["rank_dynamical_genes"]
 
-          for cluster in df.columns:
-            #df[0:1].values.ravel()[:12] ### by row
-            scv.pl.scatter(adata, color=group_by,palette=palette, basis=df[cluster].values[:top_n],vkey=vkey, size=10, linewidth=2, alpha=1, ylabel="cluster: "+cluster+"\nunspliced",
-                              add_linfit=True, add_rug=True, add_outline=True, ncols=3, frameon=True, save=False, show=False)
+          for cluster in df1.columns:
+            #df1[0:1].values.ravel()[:12] ### by row
+            scv.pl.scatter(adata, color=group_by,palette=palette, basis=df1[cluster].values[:top_n],vkey=vkey, size=10, linewidth=2, alpha=1, ylabel="cluster: "+cluster+"\nunspliced",
             if show_plot is True:
               plt.show()
             if save:
               plt.savefig('.'.join(filter(None, [fileprefix, cluster, vkey+"_genes1.png"])), dpi=dpi)
 
-            scv.pl.velocity(adata, color=group_by, var_names=df[cluster].values[:top_n],vkey=vkey, size=10, linewidth=2, alpha=1, ylabel="cluster: "+cluster+"\nunspliced", 
+            scv.pl.velocity(adata, color=group_by, var_names=df1[cluster].values[:top_n],vkey=vkey, size=10, linewidth=2, alpha=1, ylabel="cluster: "+cluster+"\nunspliced", 
                              add_outline=True,basis=basis, color_map=["Blues", "YlOrRd"], ncols=2, save=False, show=False)
             if show_plot is True:
               plt.show()