He, Peng 何鹏

Visium data visualization: enabling histology image to be overlaid and co-zoommed[FEATURE REQUEST]

27

I have 10X Visium data for a spatial transcriptomics project. Although I'm able to use the spatial coordinates for the cellxgene embedding, I'm not able to put the image on...

Above error raised while reading key '/layers' of type <class 'h5py._hl.group.Group'>

1

I'm using scanpy 1.8.2, anndata 0.8.0 and h5py 3.1.0 I got this error while reading an h5ad file: ``` adata=sc.read_h5ad('XXXX.h5ad') --------------------------------------------------------------------------- KeyError Traceback (most recent call last) /opt/conda/lib/python3.8/site-packages/anndata/_io/utils.py in func_wrapper(elem,...

KeyError: 1 in read_10x_mtx if genes.tsv has only one column

8

I have a similar issue to [this comment](https://github.com/theislab/scanpy/issues/1916#issuecomment-927497782). `Carraro=sc.read_10x_mtx('/mnt/Carraro',var_names='gene_ids')` Switching to `gene_symbols` didn't work Error messages: ``` --> This might be very slow. Consider passing `cache=True`, which enables much faster...

Public function for accessing category colors

3

I noticed that the order of .uns['leiden_colors'] might have changed. Previously I had a set of codes to extract color codes from that attribute and save into a dictionary. May...

undefined symbol: H5Pset_fapl_ros3

3

I'm using linux but have this problem! I followed this issue but it couldn't help me solve this. https://github.com/scverse/scvi-tools/issues?q=H5Pset_fapl_ros3#issue-1235458517 ``` import scvi --------------------------------------------------------------------------- ImportError Traceback (most recent call last) Input...

### Description Error using axescenter (line 107) AXESCENTER does not work for log scaled or 3D axes. See help #### Steps to Reproduce 1. plot3(1:100,sin([1:100]/5),cos([1:100]/5)) 2. axescenter() | OS version...

I got this error when running `read_zarr` ``` --------------------------------------------------------------------------- NameError Traceback (most recent call last) /tmp/ipykernel_14805/1560565781.py in ----> 1 iss=anndata.read_zarr("https://b.cog.sanger.ac.uk/datasets/ISS/0.0.1/anndata.zarr") ~/miniconda3/envs/flng/lib/python3.8/site-packages/anndata/_io/read.py in read_zarr(*_, **__) 24 25 def read_zarr(*_, **__): --->...

cluster_genotypes.vcf misses one cluster

3

I ran the whole pipeline using: ``` singularity exec -B $PWD ~/tools/souporcell/souporcell.sif souporcell_pipeline.py \ -i possorted_genome_bam.bam -b filtered_feature_bc_matrix/barcodes.tsv.gz \ -f ~/refseq/refdata-cellranger-GRCh38-3.0.0/fasta/genome.fa -t 15 -o souporcell \ --common_variants ~/tools/souporcell/jbID.noGenotypes.vcf --skip_remap True...

<simpleError in checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon): NAs found in the working weights variable 'wz'>

22

Hi Cole and Xiaojie, I was running plot_pseudotime_heatmap. And I got that error message although it indeed gave me a figure. The error message is: It looks like [some of...

Error in tobit(): could not find function "tobit"

3

I was trying to convert a Seurat object to a Monocle3 object. But the importCDS function threw that error. Any ideas?