plotQCSummary

Plots the distributions of QC metrics and their cutoffs.

Usage

plotQCSummary(
  object,
  qc.metrics = c("cellqc_signal.sum", "cellqc_DNA", "cellqc_cell.size",
    "cellqc_signal.cv", "cellqc_normalized.signal.sum", "cellqc_num.markers",
    "cellqc_dist.n", "cellqc_dist.smooth"),
  group.variable = "experiment_label",
  include.thresholds = TRUE
)

Arguments

object

A SpatialMap object

qc.metrics

The list of QC metrics to plot. Will be filtered by columns present in cellMetadata

group.variable

How to group the results (e.g. by region, sample, experiment)? Each group will be represented by a density curve in the plots. Must match a column in object's cellMetadata (often derived from projectMetadata following a call to mergeProjectMetadata).

include.thresholds

Whether to add red vertical lines on plot and print thresholds values in the caption. These values are derived from thresholds in settings.

Value

A list of ggplot objects, one for each of the qc.metrics specified (with existing data calculated by QCMetrics).

Details

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

See also

QCMetrics()