Open ccshao opened 2 years ago
First thanks for the nice tool!
I was trying to mapping two scATAC-seq data, eg, ko to wt, with stream v1.0
In both datasets I used the precomputated UMAP projections. The codes for wt is shown bellow, in which the steps on add umap were taken from https://github.com/pinellolab/STREAM/issues/100#issuecomment-746414477.
import stream as st import pandas as pd st.__version__ st.set_figure_params(dpi=300, style='white', figsize=[5.4, 4.8], rc={'image.cmap': 'viridis'}) adata = st.read(file_name='wt_counts.tsv.gz', workdir='./result_atac') st.add_cell_labels(adata, file_name='wt_cell_label.tsv') st.add_cell_colors(adata, file_name='wt_cell_label_col.tsv') st.cal_qc(adata, assay='atac') st.normalize(adata, method='tf_idf') st.select_top_principal_components(adata, first_pc=False, n_pc=50, save_fig=True) #- Precompuated umap. umap_res = pd.read_csv("wt_umap.csv", sep="\t") adata.obsm['X_dr'] = umap_res.to_numpy() adata.obsm['X_vis_umap'] = umap_res.to_numpy() st.plot_visualization_2D(adata, n_neighbors=100, color=['label'], use_precomputed=True, save_fig=True) st.seed_elastic_principal_graph(adata, n_clusters=3, use_vis=True) st.elastic_principal_graph(adata, epg_alpha=0.05)
However, when trying to align ko to wt:
adata_wt = st.read(file_name='CR_wt_atac_peaks.pkl') adata_ko = st.read(file_name='CR_ko_atac_peaks.pkl') adata_all = st.map_new_data(adata_wt, adata_ko)
Got the error:
Traceback (most recent call last): File "", line 1, in File "/home/shao/miniconda3/envs/env_stream/lib/python3.7/site-packages/stream/core.py", line 4040, in map_new_data feature = adata_ref.uns['params']['dimension_reduction']['feature'] KeyError: 'dimension_reduction'
In the source, I saw there is an transform step.
if(method == 'umap'): if('trans_umap' in adata_ref.uns_keys()): trans = adata_ref.uns['trans_umap'] adata_new.obsm['X_umap_mapping'] = trans.transform(input_data) adata_new.obsm['X_dr'] = adata_new.obsm['X_umap_mapping'].copy() else: raise Exception("Please run 'st.dimension_reduction()' using 'umap' first.")
As I am using the precompuated umap, how could I instruct stream to use that projection?
stream
Thanks and I am happy to provide more details if needed!
First thanks for the nice tool!
I was trying to mapping two scATAC-seq data, eg, ko to wt, with stream v1.0
In both datasets I used the precomputated UMAP projections. The codes for wt is shown bellow, in which the steps on add umap were taken from https://github.com/pinellolab/STREAM/issues/100#issuecomment-746414477.
However, when trying to align ko to wt:
Got the error:
In the source, I saw there is an transform step.
As I am using the precompuated umap, how could I instruct
stream
to use that projection?Thanks and I am happy to provide more details if needed!