Codeplot
Introduction
Script
Input
Output
pca
Introduction

this workflow normalize counts per cell and ogarithmize the data matrix by scanpy.pp.normalize_total and scanpy.pp.log1p

Script
Input
Task nameAttribute nameTypeDescription
*
      main
    project_nameString
      project name
    
*
      main
    anndataFile
      Input object format：anndata
    
*
      main.pca
    zero_centerBoolean
      If True, compute standard PCA from covariance matrix. If False, omit zero-centering variables (uses TruncatedSVD), which allows to handle sparse input efficiently. Passing None decides automatically based on sparseness of the data.
    
*
      main.pca
    use_highly_variableBoolean
      Whether to use highly variable genes only, stored in .var['highly_variable']. By default uses them if they have been determined beforehand.
    
*
      main.pca
    svd_solverString
      method of SVD solver to use
    
*
      main.pca
    n_compsInt
      Number of principal components to compute. Defaults to 50, or 1 - minimum dimension size of selected representation.
    
*
      main.pca
    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.pca
    dockerString
      --
    
*
      main.pca
    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
    pngfileArray[File]
      Return the output file to the column name of the corresponding table by this.xxx
    
*
      main
    h5adfileFile
      Return the output file to the column name of the corresponding table by this.xxx