Additional information

• Monocle3 stores identifying information about certain objects and their sources, and includes matrix checksums and dimensions. Use the command identity_table(cds) to view this information. For example,

   > cds <- load_worm_embryo()
   > cds <- preprocess_cds(cds, build_nn_index=TRUE)
   > cds <- reduce_dimension(cds, build_nn_index=TRUE)
   No preprocess_method specified, using preprocess_method = 'PCA'
   > identity_table(cds)
  Count matrix identity
    matrix_id: 7f6a56c3933802a4631c15109e6501c5  dim: 20222 6188
    matrix_type: URL: https://depts.washington.edu:/trapnell-lab/software/monocle3/celegans/data/packer_embryo_expression.rds
  
  Reduced dimension matrix identity
    PCA
      matrix_type matrix:PCA
      matrix_id   9fb8819fac058c01a6044a2235991588  dim: 6188 50
      prev_matrix_type    URL: https://depts.washington.edu:/trapnell-lab/software/monocle3/celegans/data/packer_embryo_expression.rds
      prev_matrix_id      7f6a56c3933802a4631c15109e6501c5  dim: 20222 6188
      model_type  matrix:PCA
      model_id    9fb8819fac058c01a6044a2235991588  dim: 6188 50
  
      .
      .
      .
  
    UMAP
      matrix_type matrix:UMAP
      matrix_id   8a52b66ee33e4dad7c9c5310525821ec  dim: 6188 2
      prev_matrix_type    matrix:PCA
      prev_matrix_id      9fb8819fac058c01a6044a2235991588  dim: 6188 50
      model_type  matrix:UMAP
      model_id    8a52b66ee33e4dad7c9c5310525821ec  dim: 6188 2
            

• On startup, Monocle3 runs commands in the file $HOME/.monoclerc, if it exists. You can customize Monocle3 behavior by setting global variables in it. For example, if you want Monocle3 to use BPCells matrices, GNU tar, and not tar monocle objects directories by default, create $HOME/.monoclerc with the following function calls

  # Use BPCells matrix_class for new matrices.
  monocle3:::set_global_variable('matrix_class_default', 'BPCells')
  # Don't tar monocle objects directories when running save_monocle_objects.
  monocle3:::set_global_variable('archive_control', list(archive_type='none', archive_compression='none'))
  # Use gnu tar for R tar. This affects the save_monocle_objects() function
  # when it makes a tar archive.
  Sys.setenv('tar' = paste(Sys.getenv("TAR"), "-H", "gnu"))
             

  The function .onLoad() in the file R/zzz.R runs the code in $HOME/.monoclerc on startup. Default global variable values are defined in .onLoad() before sourcing $HOME/.monoclerc, so you can change the defaults by setting them in $HOME/.monoclerc.

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