plotQC: Quality Control Plots

In WeiSong-bio/roryk-bcbioSinglecell: Single-Cell RNA-Seq Utilities

Description

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

Usage

## 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

• grid: cowplot::plot_grid() graphical output.

• list: list containing ggplot objects.

• markdown: R Markdown report, with reports separated by headers.

Author(s)

Michael Steinbaugh

See Also

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

Examples

# bcbioSingleCell ====
plotQC(indrops_small)

# SingleCellExperiment ====
plotQC(cellranger_small)

# seurat ====
plotQC(seurat_small)

WeiSong-bio/roryk-bcbioSinglecell documentation built on July 6, 2019, 12:03 a.m.