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Develop #184

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merged 2 commits into from
Oct 23, 2023
Merged

Develop #184

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e2041b0
fix a bug in RunSCVELO
zhanghao-njmu Oct 23, 2023
f1abf54
conflict fixed
zhanghao-njmu Oct 23, 2023
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9 changes: 4 additions & 5 deletions inst/python/SCP_analysis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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()
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