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
$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
.