MVP.Report.QQplot: QQ Plot

In XiaoleiLiuBio/MVP: Memory-Efficient, Visualize-Enhanced, Parallel-Accelerated GWAS Tool

QQ Plot

Description

QQ Plot

Usage

MVP.Report.QQplot(
  P.values,
  taxa_name,
  col = c("blue"),
  cex = 0.5,
  threshold = NULL,
  amplify = TRUE,
  signal.col = "red",
  signal.pch = 19,
  signal.cex = 0.8,
  conf.int = TRUE,
  cex.axis = 1,
  conf.int.col = "grey",
  threshold.col = "red",
  outpath = getwd(),
  file.type = "jpg",
  memo = "MVP",
  box = TRUE,
  dpi = 300,
  file.output = TRUE,
  verbose = TRUE
)

Arguments

P.values	P values
taxa_name	The identifier of the phenotype will be used to generate a portion of the image file name. If the title parameter is NULL, it will also be part of the title.
col	default color is "blue"
cex	A numerical value giving the amount by which plotting text and symbols should be magnified relative to the default. This starts as 1 when a device is opened, and is reset when the layout is changed, e.g. by setting mfrow. see par.
threshold	Number or Vector. The cutoff line on Manhattan plot, e.g. Bonfferoni correction. More than one significant line can be added onto one figure. If threshold=0 or NULL, the threshold line will not be added.
amplify	Logical value. If TRUE, the points that passed the threshold line will be highlighted
signal.col	Character. If "amplify" is TRUE, "signal.col" is used to set the color of significant points, if "signal.col" is NULL, the colors of significant points will not be changed
signal.pch	Number. If "amplify" is TRUE, users can set the type of significant points
signal.cex	Number. If "amplify" is TRUE, "signal.cex" is used to set the size of significant points
conf.int	Whether to draw a confidence interval
cex.axis	a number, controls the size of numbers of X-axis and the size of labels of circle plot.
conf.int.col	a character, the color of the confidence interval on QQ-plot.
threshold.col	Character or Vector. The colors of threshold lines
outpath	Only when file.output = TRUE, determines the path of the output file
file.type	A string or NULL is used to determine the type of output file. Can be "jpg", "pdf", "tiff". If it is NULL, it will use dev.new() to create a new graphics device in the current environment, which may be RStudioGD or the default device of the system.
memo	the prefix of the output image file.
box	A Boolean value that controls whether to draw a box around QQplot.
dpi	a number, the picture element for .jpg and .tiff files. The default is 300.
file.output	Logical value. If TRUE, the figures will be generated.
verbose	whether to print detail.

Value

Output file: <memo>.QQplot.<taxa_name>.<type>

Examples

data(pig60K, package = "rMVP")

MVP.Report(pig60K[1:10000,], plot.type="q", file.output=FALSE)

XiaoleiLiuBio/MVP documentation built on Sept. 27, 2024, 7:44 a.m.