MapQuery: Map query cells to a reference

Description

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.

Usage

MapQuery(
  anchorset,
  query,
  reference,
  refdata = NULL,
  new.reduction.name = NULL,
  reference.reduction = NULL,
  reference.dims = NULL,
  query.dims = NULL,
  reduction.model = NULL,
  transferdata.args = list(),
  integrateembeddings.args = list(),
  projectumap.args = list(),
  verbose = TRUE
)

Value

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

Arguments

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:

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.

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

reduction.model

DimReduc object that contains the umap model

transferdata.args

A named list of additional arguments to TransferData

integrateembeddings.args

A named list of additional arguments to IntegrateEmbeddings

projectumap.args

A named list of additional arguments to ProjectUMAP

verbose

Print progress bars and output