RunHarmony.SingleCellExperiment {harmony} | R Documentation |
Applies harmony on PCA cell embeddings of a SingleCellExperiment.
Description
Applies harmony on PCA cell embeddings of a SingleCellExperiment.
Usage
## S3 method for class 'SingleCellExperiment'
RunHarmony(
object,
group.by.vars,
dims.use = NULL,
verbose = TRUE,
reduction.save = "HARMONY",
...
)
Arguments
object |
SingleCellExperiment with the PCA reducedDim cell embeddings populated
|
group.by.vars |
the name(s) of covariates that harmony will remove
its effect on the data.
|
dims.use |
a vector of indices that allows only selected cell embeddings
features to be used.
|
verbose |
enable verbosity
|
reduction.save |
the name of the new slot that is going to be created by
harmony. By default, HARMONY.
|
... |
Arguments passed on to RunHarmony.default
theta Diversity clustering penalty parameter. Specify for
each variable in vars_use Default theta=2. theta=0 does not
encourage any diversity. Larger values of theta result in more
diverse clusters.
sigma Width of soft kmeans clusters. Default
sigma=0.1. Sigma scales the distance from a cell to cluster
centroids. Larger values of sigma result in cells assigned to
more clusters. Smaller values of sigma make soft kmeans cluster
approach hard clustering.
lambda Ridge regression penalty. Default lambda=1. Bigger
values protect against over correction. If several covariates
are specified, then lambda can also be a vector which needs to
be equal length with the number of variables to be
corrected. In this scenario, each covariate level group will be
assigned the scalars specified by the user. If set to NULL,
harmony will start lambda estimation mode to determine lambdas
automatically and try to minimize overcorrection (Use with caution still
in beta testing).
nclust Number of clusters in model. nclust=1 equivalent to
simple linear regression.
max_iter Maximum number of rounds to run Harmony. One round
of Harmony involves one clustering and one correction step.
early_stop Enable early stopping for harmony. The
harmonization process will stop when the change of objective
function between corrections drops below 1e-4
ncores Number of processors to be used for math operations
when optimized BLAS is available. If BLAS is not supporting
multithreaded then this option has no effect. By default,
ncore=1 which runs as a single-threaded process. Although
Harmony supports multiple cores, it is not optimized for
multithreading. Increase this number for large datasets iff
single-core performance is not adequate.
plot_convergence Whether to print the convergence plot of
the clustering objective function. TRUE to plot, FALSE to
suppress. This can be useful for debugging.
.options Advanced parameters of RunHarmony. This must be the
result from a call to 'harmony_options'. See ?'harmony_options'
for more details.
|
Value
SingleCellExperiment object. After running RunHarmony, the corrected
cell embeddings can be accessed with reducedDim(object, "Harmony").
See Also
Other RunHarmony:
RunHarmony.Seurat()
,
RunHarmony.default()
,
RunHarmony()
Examples
## Not run:
## sce is a SingleCellExperiment R object
sce <- RunHarmony(sce, "donor_id")
## End(Not run)
[Package
harmony version 1.2.0
Index]