Working with SeqFish dataΒΆ
[1]:
import stlearn as st
The data is downloaded from https://www.spatialomics.org/SpatialDB/download.php
Read SeqFish data and we select field 5.
[2]:
data = st.ReadSeqFish(count_matrix_file="../Downloads/seqfish_30911168/cortex_svz_counts.matrix",
spatial_file="../Downloads/seqfish_30911168/cortex_svz_cellcentroids.csv",
field=5)
D:\Anaconda3\envs\test2\lib\site-packages\anndata-0.7.3-py3.8.egg\anndata\_core\anndata.py:119: ImplicitModificationWarning: Transforming to str index.
warnings.warn("Transforming to str index.", ImplicitModificationWarning)
Quality checking for the data
[3]:
st.pl.QC_plot(data)
Plot gene Nr4a1
[4]:
st.pl.gene_plot(data,genes="Nr4a1")
Running Preprocessing for MERFISH data
[5]:
st.pp.filter_genes(data,min_cells=3)
st.pp.normalize_total(data)
st.pp.log1p(data)
st.pp.scale(data)
Normalization step is finished in adata.X
Log transformation step is finished in adata.X
Scale step is finished in adata.X
Running PCA to reduce the dimensions to 50
[6]:
st.em.run_pca(data,n_comps=50,random_state=0)
PCA is done! Generated in adata.obsm['X_pca'], adata.uns['pca'] and adata.varm['PCs']
Perform Louvain clustering
[7]:
st.pp.neighbors(data,n_neighbors=25)
D:\Anaconda3\envs\test2\lib\site-packages\umap_learn-0.4.3-py3.8.egg\umap\spectral.py:4: NumbaDeprecationWarning: No direct replacement for 'numba.targets' available. Visit https://gitter.im/numba/numba-dev to request help. Thanks!
import numba.targets
Created k-Nearest-Neighbor graph in adata.uns['neighbors']
[8]:
st.tl.clustering.louvain(data)
Applying Louvain clustering ...
Louvain clustering is done! The labels are stored in adata.obs['louvain']
[9]:
st.pl.cluster_plot(data,use_label="louvain",spot_size=10)
