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Description
Hello, thanks for the amazing tool. And recent days when I run tutorial, I found that the gene is not filtered out using Preprocessor. See below:
adata = dyn.sample_data.zebrafish()
|-----> Downloading data to ./data/zebrafish.h5ad
|-----> File ./data/zebrafish.h5ad already exists.
xxxx/lib/python3.10/site-packages/anndata/_core/anndata.py:1756: UserWarning: Observation names are not unique. To make them unique, call .obs_names_make_unique
.
utils.warn_names_duplicates("obs")
adata
AnnData object with n_obs × n_vars = 4181 × 16940
obs: 'split_id', 'sample', 'Size_Factor', 'condition', 'Cluster', 'Cell_type', 'umap_1', 'umap_2', 'batch'
layers: 'spliced', 'unspliced'
preprocessor = dyn.pp.Preprocessor(cell_cycle_score_enable=True)
preprocessor.preprocess_adata(adata, recipe='monocle')
|-----> Running monocle preprocessing pipeline...
|-----------> filtered out 14 outlier cells
a|-----------> filtered out 12746 outlier genes
data
|-----> PCA dimension reduction
|-----> X_pca to obsm in AnnData Object.
|-----> computing cell phase...
adata
AnnData object with n_obs × n_vars = 4167 × 16940
obs: 'split_id', 'sample', 'Size_Factor', 'condition', 'Cluster', 'Cell_type', 'umap_1', 'umap_2', 'batch', 'nGenes', 'nCounts', 'pMito', 'pass_basic_filter', 'spliced_Size_Factor', 'initial_spliced_cell_size', 'initial_cell_size', 'unspliced_Size_Factor', 'initial_unspliced_cell_size', 'ntr', 'cell_cycle_phase'
var: 'nCells', 'nCounts', 'pass_basic_filter', 'score', 'log_m', 'log_cv', 'frac', 'use_for_pca', 'ntr'
uns: 'pp', 'velocyto_SVR', 'feature_selection', 'PCs', 'explained_variance_ratio_', 'pca_mean', 'cell_phase_order', 'cell_phase_genes'
obsm: 'X_pca', 'cell_cycle_scores'
layers: 'spliced', 'unspliced', 'X_spliced', 'X_unspliced'
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