plotQC {SeqSQC} | R Documentation |
Plot QC results.
plotQC(seqfile, QCstep = c("MissingRate", "SexCheck", "Inbreeding", "IBD", "PCA"), interactive = FALSE, sdcoef = 5, pc1 = "EV1", pc2 = "EV2", pairedScatter = FALSE, ...)
seqfile |
SeqSQC object with QC results. |
QCstep |
which QC step the user want to do plotting. Takes
values of |
interactive |
whether to generate interactive plot. Recommend
to use |
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. |
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.
Qian Liu qliu7@buffalo.edu
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