MVP.Report.QQplot {rMVP}

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)