ValueError

[tongjiezhao]

Hi I got this error when running hs = hotspot.Hotspot(
... adata,
... layer_key="csc_counts",
... model='bernoulli',
... latent_obsm_key="spatial",
... umi_counts_obs_key="total_counts",
... )

Traceback (most recent call last):
File "", line 1, in
File "python3.8/site-packages/hotspot/hotspot.py", line 135, in init
raise ValueError(
ValueError:
Detected all zero genes. Please filter adata and reinitialize.

and I try

sc.pp.filter_cells(adata, min_genes=200)
sc.pp.filter_genes(adata, min_cells=3)

it still shows this error
my anndata looks like this
AnnData object with n_obs × n_vars = 1404 × 29522
obs: 'n_genes', 'total_counts'
var: 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std', 'n_cells'
uns: 'hvg', 'log1p', 'neighbors', 'pca'
obsm: 'X_pca', 'spatial'
varm: 'PCs'
layers: 'csc_counts'
obsp: 'connectivities', 'distances'
and adata.X looks like this
(0, 0) -9.273971
(1, 0) -1.1690428
(2, 0) -2.1527452
(3, 0) 0.29593784
(4, 0) 2.888746
(5, 0) -0.5670085
(6, 0) 0.022515705
(7, 0) -0.3287619
(8, 0) -0.60607976
(9, 0) 3.9856915
(10, 0) 0.59192413
(11, 0) 5.258427
(12, 0) 0.060307246
(13, 0) 0.1517446
(14, 0) 0.29431388
(15, 0) -15.718134
(16, 0) 6.711702
(17, 0) -5.2702594
(18, 0) 0.48261452
(19, 0) 2.9903271
(20, 0) 8.463634
(21, 0) 1.5748714
(22, 0) 1.0938092
(23, 0) 0.44068232
(24, 0) 1.1826563

[Polligator]

encountered the same error, did you figure out how to resolve it?

[coleruoff]

I am also encountering this issue...

[Polligator]

One workaround for me was to filter the cell and genes with higher cutoffs, like set min_cell to 20, you just need to tweak on the values.

[deto]

Hi everyone, it's hard to guess at what's happening here without your data/code, but if we extract the relevant bits in hotspot.py the check for this essentially does:

counts = adata.layers[layer_key] if layer_key is not None else adata.X
counts = counts.transpose()
valid_genes = counts.sum(axis=1) > 0
n_invalid = counts.shape[0] - valid_genes.sum()
if n_invalid > 0:
     raise ValueError(
          "\nDetected all zero genes. Please filter adata and reinitialize."
     )

So as long you had done filtering with sc.pp.filter_genes and min_cell >= 1 it should pass as all remaining genes should have a nonzero sum when summing across cells. Maybe you can run that snippet on your anndata object and it will shed light on why it's not passing the check?

[liuxiawei]

I think this problem is caused by the layer name. I found the sc.pp.filter_genes only filter counts layer. when use other layer, The problem happend