scverse / scverse/scanpy

The seurat converted into anndata to analyze the trajectory inference occurred the weird circumstance

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Description

Hi ,
In my case, the seurat object using the sceasy algorithm to transfer into anndata object for trajectory inference analysis.
The code lying below:
import numpy as np
import pandas as pd
import matplotlib.pyplot as pl
from matplotlib import rcParams
import scanpy as sc
sc.pp.recipe_zheng17(adata)
sc.tl.pca(adata, svd_solver='arpack')
sc.pp.neighbors(adata, n_neighbors=4, n_pcs=20)
sc.tl.draw_graph(adata)
sc.pl.draw_graph(adata, color='paul15_clusters', legend_loc='on data')
The picture showing confused result posted below:

The object information:

adata
AnnData object with n_obs × n_vars = 17885 × 999
obs: 'orig.ident', 'nCount_RNA', 'nFeature_RNA', 'percent.mt', 'RNA_snn_res.0.5', 'seurat_clusters', 'pANN_0.25_0.02_752', 'DF.classifications_0.25_0.02_752', 'percent.rp', 'pANN_0.25_0.02_826', 'DF.classifications_0.25_0.02_826', 'group', 'celltype', 'n_counts_all'
var: 'vst.mean', 'vst.variance', 'vst.variance.expected', 'vst.variance.standardized', 'vst.variable', 'n_counts', 'mean', 'std'
uns: 'seurat_clusters_colors', 'log1p', 'pca', 'neighbors', 'draw_graph'
obsm: 'X_pca', 'X_tsne', 'X_umap', 'X_draw_graph_fr'
varm: 'PCs'
obsp: 'distances', 'connectivities'

Contributor guide

Open the contributing guide

First steps

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  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing the supplied AnnData conversion and preprocessing sequence with the listed 17,885-cell object. Inspect the converted metadata, PCA, neighbor graph, and draw_graph outputs to determine which step produces the unexpected result. Done means identifying an actionable cause or confirming the required conversion or analysis settings.

Written by the indexing model from the issue text.

Assessment

Tech stack
matplotlib, numpy, pandas, python
Domain
bioinformatics, data-visualization
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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