plotQC: Quality Control Plots

Description Usage Arguments Value Author(s) See Also Examples

Description

Utility function that loops our standard quality control plots, for easy visualization.

Usage

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## S4 method for signature 'SingleCellExperiment'
plotQC(object, interestingGroups,
  geom = c("ecdf", "ridgeline", "violin", "histogram", "boxplot"),
  headerLevel = 2L, legend = FALSE, return = c("grid", "list",
  "markdown"))

## S4 method for signature 'seurat'
plotQC(object, interestingGroups, geom = c("ecdf",
  "ridgeline", "violin", "histogram", "boxplot"), headerLevel = 2L,
  legend = FALSE, return = c("grid", "list", "markdown"))

Arguments

object

Object.

interestingGroups

Character vector of interesting groups. Must be formatted in camel case and intersect with sampleData() colnames.

geom

Plot type. Uses match.arg() and defaults to the first argument in the vector.

headerLevel

R Markdown header level.

legend

Include plot legend.

return

Return type. Uses base::match.arg() internally and defaults to the first argument in the vector.

Value

Author(s)

Michael Steinbaugh

See Also

Other Quality Control Functions: barcodeRanksPerSample, filterCells, metrics, plotCellCounts, plotGenesPerCell, plotMitoRatio, plotMitoVsCoding, plotNovelty, plotReadsPerCell, plotUMIsPerCell, plotZerosVsDepth

Examples

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# bcbioSingleCell ====
plotQC(indrops_small)

# SingleCellExperiment ====
plotQC(cellranger_small)

# seurat ====
plotQC(seurat_small)

roryk/bcbioSinglecell documentation built on May 27, 2019, 10:44 p.m.