View source: R/dimension_reduction.R
runUMAP | R Documentation |
run UMAP
runUMAP(
gobject,
feat_type = NULL,
spat_unit = NULL,
expression_values = c("normalized", "scaled", "custom"),
reduction = c("cells", "feats"),
dim_reduction_to_use = "pca",
dim_reduction_name = NULL,
dimensions_to_use = 1:10,
name = NULL,
feats_to_use = NULL,
genes_to_use = NULL,
return_gobject = TRUE,
n_neighbors = 40,
n_components = 2,
n_epochs = 400,
min_dist = 0.01,
n_threads = NA,
spread = 5,
set_seed = TRUE,
seed_number = 1234,
verbose = T,
toplevel_params = 2,
...
)
gobject |
giotto object |
feat_type |
feature type |
spat_unit |
spatial unit |
expression_values |
expression values to use |
reduction |
cells or genes |
dim_reduction_to_use |
use another dimension reduction set as input |
dim_reduction_name |
name of dimension reduction set to use |
dimensions_to_use |
number of dimensions to use as input |
name |
arbitrary name for UMAP run |
feats_to_use |
if dim_reduction_to_use = NULL, which genes to use |
genes_to_use |
deprecated, use feats_to_use |
return_gobject |
boolean: return giotto object (default = TRUE) |
n_neighbors |
UMAP param: number of neighbors |
n_components |
UMAP param: number of components |
n_epochs |
UMAP param: number of epochs |
min_dist |
UMAP param: minimum distance |
n_threads |
UMAP param: threads/cores to use |
spread |
UMAP param: spread |
set_seed |
use of seed |
seed_number |
seed number to use |
verbose |
verbosity of function |
toplevel_params |
parameters to extract |
... |
additional UMAP parameters |
See umap
for more information about these and other parameters.
Input for UMAP dimension reduction can be another dimension reduction (default = 'pca')
To use gene expression as input set dim_reduction_to_use = NULL
If dim_reduction_to_use = NULL, genes_to_use can be used to select a column name of
highly variable genes (see calculateHVF
) or simply provide a vector of genes
multiple UMAP results can be stored by changing the name of the analysis
giotto object with updated UMAP dimension reduction
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