Codeplot
Introduction
Script
Input
Output
neighbors
Introduction

compute a neighborhood graph of observations by sc.pp.neighbors

Script
Input
Task nameAttribute nameTypeDescription
*
      main
    project_nameString
      project name
    
*
      main
    anndataFile
      Input object format：anndata
    
*
      main.neighbors
    use_repString
      Use the indicated representation. 'X' or any key for .obsm is valid. If None, the representation is chosen automatically: For .n_vars < 50, .X is used, otherwise ‘X_pca’ is used. If ‘X_pca’ is not present, it’s computed with default parameters.
    
*
      main.neighbors
    n_pcsInt
      Use this many PCs. If n_pcs==0 use .X if use_rep is None
    
*
      main.neighbors
    n_neighborsInt
      The size of local neighborhood (in terms of number of neighboring data points) used for manifold approximation. Larger values result in more global views of the manifold, while smaller values result in more local data being preserved. In general values should be in the range 2 to 100. If knn is True, number of nearest neighbors to be searched. If knn is False, a Gaussian kernel width is set to the distance of the n_neighbors neighbor.
    
*
      main.neighbors
    methodString
      Use 'umap'  or 'gauss'  for computing connectivities. Use 'rapids' for the RAPIDS implementation of UMAP (experimental, GPU only).
    
*
      main.neighbors
    memoryString
      Number of memory running tasksnotice:1. The value range is 0.25-32 cores, in addition, 48 cores and 64 cores can be selected, and the CPU must be an integer multiple of 0.25 cores; 2. The memory value range is 1GB-512GB, and the memory must be an integer multiple of 1GB. 3. The CPU / memory ratio must be between 1:2 and 1:8
    
*
      main.neighbors
    knnBoolean
      If True, use a hard threshold to restrict the number of neighbors to n_neighbors, that is, consider a knn graph. Otherwise, use a Gaussian Kernel to assign low weights to neighbors more distant than the n_neighbors nearest neighbor.
    
*
      main.neighbors
    key_addedString
      If not specified, the neighbors data is stored in .uns[‘neighbors’], distances and connectivities are stored in .obsp[‘distances’] and .obsp[‘connectivities’] respectively. If specified, the neighbors data is added to .uns[key_added], distances are stored in .obsp[key_added+’_distances’] and connectivities in .obsp[key_added+’_connectivities’].
    
*
      main.neighbors
    dockerString
      --
    
*
      main.neighbors
    cpuString
      Number of CPU running tasks.notice:1. The value range is 0.25-32 cores, in addition, 48 cores and 64 cores can be selected, and the CPU must be an integer multiple of 0.25 cores; 2. The memory value range is 1GB-512GB, and the memory must be an integer multiple of 1GB. 3. The CPU / memory ratio must be between 1:2 and 1:8
    
Output
Task nameAttribute nameTypeDescription
*
      main
    h5adfileFile
      Return the output file to the column name of the corresponding table by this.xxx