Incorrect number setting ofr highly_variable_genes about scanpy HOT 8 CLOSED

Hi, I don’t see any errors in your example. Can you please specify what you expected to happen and how what happened differs from that?

Also please provide code as text (in a Markdown code block), not as images.

from scanpy.

Hi, I intend to have 13634 hvgs, but it gave me 13652 genes. I am curious about the difference. Is it a bug?

Code:

adata_atac.X = (adata_atac.X > 0)*1
sc.pp.highly_variable_genes(adata_atac, n_top_genes=13634)
adata_atac = adata_atac[:,adata_atac.var['highly_variable']]

from scanpy.

Could have all kinds of reasons. Genes sharing the same score, duplicate gene names.

We won’t be able to tell without a reproducible example.

from scanpy.

If it is caused by the same score, how to ensure the uniquenss? Thanks. I did not receive the var.unique.name error thus I think it was not caused by duplicate gene names

It is neurips 2021 single cell competition dataset.

from scanpy.

I’ll take a look if you update your issue with a code block that I can copy, that will download the dataset and then reproduce the error without me having to go to any website and download anything manually.

from scanpy.

Thanks. The dataset is here:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE194122

Sicne it is from GSE, I think it is easy to download and it is formed into h5ad format (the multiome part).
GSE194122_openproblems_neurips2021_multiome_BMMC_processed.h5ad.gz

Code:

adata_atac.X = (adata_atac.X > 0)*1
sc.pp.highly_variable_genes(adata_atac, n_top_genes=13634)
adata_atac = adata_atac[:,adata_atac.var['highly_variable']]

from scanpy.

So this would be a reproducible example:

import gzip
import shutil
from urllib.request import urlopen
from pathlib import Path

from tqdm.notebook import tqdm
import scanpy as sc

url = "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE194122&format=file&file=GSE194122%5Fopenproblems%5Fneurips2021%5Fmultiome%5FBMMC%5Fprocessed%2Eh5ad%2Egz"

path = Path("data/GSE194122_openproblems_neurips2021_multiome_BMMC_processed.h5ad")
if not path.is_file():
    with (
        urlopen(url) as raw,
        tqdm.wrapattr(raw, "read", total=int(raw.headers["Content-Length"])) as wrapped,
        gzip.open(wrapped, 'rb') as f_in,
        path.open('wb') as f_out,
    ):
        shutil.copyfileobj(f_in, f_out)

adata_atac = sc.read(path)
adata_atac.X = (adata_atac.X > 0)*1
sc.pp.highly_variable_genes(adata_atac, n_top_genes=13634)
adata_atac = adata_atac[:,adata_atac.var['highly_variable']]

from scanpy.

Problem seems to be fixed in the newest scanpy:

from scanpy.