Files for embedding data type

Import packages

import scanpy as sc

 

Step 1

Read the .mtx file using scanpy.read_mtx which will result in an anndata file (that can be written to .h5ad)

Sample Matrix file

%%MatrixMarket matrix coordinate integer general
%
90980 20242 42994070
1 9114 1
1 14115 1
1 17826 1

 adata = sc.read_mtx("/home/ubuntu/matrix.mtx")

Step 2

Sample metadata file

 

Reading the metadata in using  using the pandas function

 

Step 3

Sample UMAP coordinate file

UMAP1,UMAP2

23399.000000,30703.000000

36861.000000,61648.000000

48900.000000,32121.000000

embeddings = pd.read_csv("/home/ubuntu/UMAP_coordinates.coords.csv")

embeddings = embeddings.to_numpy()

adata.obsm["X_umap"] = embeddings

Step 4

Writing h5ad output

adata.write("./atac.h5ad")