plotQC: Plot the QC results for specific QC steps.

In SeqSQC: A bioconductor package for sample quality check with next generation sequencing data

Description

Plot QC results.

Usage

plotQC(seqfile, QCstep = c("MissingRate", "SexCheck", "Inbreeding",
  "IBD", "PCA"), interactive = FALSE, sdcoef = 5, pc1 = "EV1",
  pc2 = "EV2", pairedScatter = FALSE, ...)

Arguments

seqfile	SeqSQC object with QC results.
QCstep	which QC step the user want to do plotting. Takes values of c("MissingRate", "SexCheck", "Inbreeding", "IBD", "PCA")
interactive	whether to generate interactive plot. Recommend to use interactive = TRUE if user perform sample QC using an rmarkdown script and output plot to html format.
sdcoef	for inbreeding outlier check, how many standard deviation we need for identification of inbreeding outliers. The default is 5.
pc1	the eigenvector on x axis for PCA result. The default is "EV1" for eigenvector 1.
pc2	the eigenvector on y axis for PCA result. The default is "EV2" for eigenvector 2.
pairedScatter	for PCA result, whether to plot the paired scatterplot for the first 4 PC axes.
...	Arguments to be passed to other methods.

Value

the ggplot or interactive plot (if output is in html format) for specific QC result. If "interactive=FALSE", it returns a ggplot and author could have the flexibility to add on any layers, scales, faceting specifications and coordinate systems.

Author(s)

Qian Liu [e-mail]

Examples

load(system.file("extdata", "example.seqfile.Rdata", package="SeqSQC"))
gfile <- system.file("extdata", "example.gds", package="SeqSQC")
seqfile <- SeqSQC(gdsfile = gfile, QCresult = QCresult(seqfile))
p <- plotQC(seqfile, QCstep="PCA", interactive=FALSE)
p

SeqSQC documentation built on Nov. 8, 2020, 5:03 p.m.