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
)
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
An AnchorSet object
Query object used in anchorset construction
Reference object used in anchorset construction
Data to transfer. This can be specified in one of two ways:
The reference data itself as either a vector where the names correspond to the reference cells, or a matrix, where the column names correspond to the reference cells.
The name of the metadata field or assay from the reference object
provided. This requires the reference parameter to be specified. If pulling
assay data in this manner, it will pull the data from the data slot. To
transfer data from other slots, please pull the data explicitly with
GetAssayData
and provide that matrix here.
Name for new integrated dimensional reduction.
Name of reduction to use from the reference for neighbor finding
Dimensions (columns) to use from reference
Dimensions (columns) to use from query
Determine if the weight and anchor matrices are stored.
DimReduc
object that contains the umap model
A named list of additional arguments to
TransferData
A named list of additional arguments to
IntegrateEmbeddings
A named list of additional arguments to
ProjectUMAP
Print progress bars and output