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rdong08 / GiniClust3

Rare cell identification tool for single cell datasets
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operands could not be broadcast? #3

Closed chansigit closed 4 years ago

chansigit commented 4 years ago

ValueError Traceback (most recent call last)

in 1 import giniclust3 as gc 2 gc.gini.calGini(adata) ###Calculate Gini Index ----> 3 adataGini=gc.gini.clusterGini(adata,neighbors=3) ###Cluster based on Gini Index ~/anaconda1907/lib/python3.7/site-packages/giniclust3/gini.py in clusterGini(adataSC, **kwargs) 231 raise SystemExit("Only leiden or louvain cluster method is allowed in this step.") 232 adataGini=adataSC[:,adataSC.var['gini']] --> 233 scaleMatrix=arctanTransform((adataGini.X)) 234 adataScaleGini=anndata.AnnData(X=scaleMatrix) 235 ~/anaconda1907/lib/python3.7/site-packages/giniclust3/gini.py in arctanTransform(matrix) 63 expM=np.mean(expSort[0:end]) 64 break ---> 65 arctan=np.arctan((transMatrix[i]-expM))*10+np.arctan(expM)*10 66 arctanExp.append(arctan) 67 arctanExp=np.array(arctanExp) ValueError: operands could not be broadcast together with shapes (1219,) (0,) Hi, I met these errors while calculating gini index, can you help me figure out why? thanks.
rdong08 commented 4 years ago

Hi, thanks for your interest for GiniClust3. Could I know what's the dimension of your input scRNA data? Did you do the filter and normalization for your dataset?