MapQuery | R Documentation |
This is a convenience wrapper function around the following three functions
that are often run together when mapping query data to a reference:
TransferData
, IntegrateEmbeddings
,
ProjectUMAP
. Note that by default, the weight.reduction
parameter for all functions will be set to the dimension reduction method
used in the FindTransferAnchors
function call used to construct
the anchor object, and the dims
parameter will be the same dimensions
used to find anchors.
MapQuery(
anchorset,
query,
reference,
refdata = NULL,
new.reduction.name = NULL,
reference.reduction = NULL,
reference.dims = NULL,
query.dims = NULL,
store.weights = FALSE,
reduction.model = NULL,
transferdata.args = list(),
integrateembeddings.args = list(),
projectumap.args = list(),
verbose = TRUE
)
anchorset |
An AnchorSet object |
query |
Query object used in anchorset construction |
reference |
Reference object used in anchorset construction |
refdata |
Data to transfer. This can be specified in one of two ways:
|
new.reduction.name |
Name for new integrated dimensional reduction. |
reference.reduction |
Name of reduction to use from the reference for neighbor finding |
reference.dims |
Dimensions (columns) to use from reference |
query.dims |
Dimensions (columns) to use from query |
store.weights |
Determine if the weight and anchor matrices are stored. |
reduction.model |
|
transferdata.args |
A named list of additional arguments to
|
integrateembeddings.args |
A named list of additional arguments to
|
projectumap.args |
A named list of additional arguments to
|
verbose |
Print progress bars and output |
Returns a modified query Seurat object containing:#'
New Assays corresponding to the features transferred and/or their
corresponding prediction scores from TransferData
An integrated reduction from IntegrateEmbeddings
A projected UMAP reduction of the query cells projected into the
reference UMAP using ProjectUMAP
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