symphony (version 0.1.2)

mapQuery: Function for mapping query cells to a Symphony reference

Description

Function for mapping query cells to a Symphony reference

Usage

mapQuery(
  exp_query,
  metadata_query,
  ref_obj,
  vars = NULL,
  verbose = TRUE,
  do_normalize = TRUE,
  do_umap = TRUE,
  sigma = 0.1
)

Value

Symphony query object. Mapping embedding is in the $Z slot. Other slots include query expression matrix ($exp), query cell-level metadata ($meta_data), query cell embedding in pre-Harmonized reference PCs ($Zq_pca), query cell soft cluster assignments ($R), and query cells in reference UMAP coordinates ($umap).

Arguments

exp_query

Query gene expression (genes by cells)

metadata_query

Query metadata (cells by attributes)

ref_obj

Reference object as returned by Symphony buildReference()

vars

Query batch variable(s) to integrate over (column names in metadata)

verbose

Verbose output

do_normalize

Perform log(CP10K+1) normalization on query expression

do_umap

Perform umap projection into reference UMAP (if reference includes a uwot model)

sigma

Fuzziness parameter for soft clustering (sigma = 1 is hard clustering)