Filter CODEX cell data

Function to filter Regions in a SpatialMap based on parameters defined in the settings(). Values for each cell must have already been computed by QCMetrics().

Usage

FilterCodex(
  object,
  recompute = T,
  remove.filtered.cells = NULL,
  analyze = NULL,
  spatial.qc = FALSE,
  qc.var = ".qc_result",
  qc.var.logical = ".pass_qc",
  custom.qc.vars = NULL,
  custom.qc.mappings = NULL,
  custom.qc.labels = NULL
)

Arguments

object

A SpatialMap object

recompute

Whether to recompute filtering results (for example, if settings have been changed)

remove.filtered.cells

Whether to remove filtered cells from the returned object.

analyze

What to analyze (and how). The options are "regions", NULL (activeAnalysis), the name of a currently existing formal analysis, or the name of a column in object's projectMetadata (an "informal" analysis).

spatial.qc

Whether to use spatial QC parameters when filtering

qc.var

The name of the QC results column in cellMetadata that will detail the QC results for each cell. Should represent a categorical variable, with values including "pass" and comma-separated reasons for why a cell failed QC (e.g., "DNA, signal sum").

qc.var.logical

The name of the QC results column in cellMetadata that will specify whether a cell passes QC. Should represent a logical variable.

custom.qc.vars

Column names of existing annotations in cellMetadata, to be used for custom QC filtering

custom.qc.mappings

Named list of lists, where names correspond to each custom.qc.vars and values to a named list of labels that should map to pass and fail. Example format: list(custom_qc1 = list(pass = c("..."), fail = c("...")), custom_qc2 = list(pass = c("..."), fail = c("...")))

custom.qc.labels

Named character vector where names correspond to each custom.qc.vars and values to the desired label used for the corresponding failing cells

Value

A SpatialMap object with some new columns added to the cellMetadata slot, named based on the values passed to the arguments qc.var and qc.var.logical. See the descriptions for those parameters for more info.

Details

See vignette("AnalysisGuide2_QC_with_SpatialMap") for a representative workflow that uses this function.

See also

QCMetrics()