MVP.Hist: Phenotype distribution histogram

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

Phenotype distribution histogram

Description

Phenotype distribution histogram

Usage

MVP.Hist(
  phe,
  col = c("dodgerblue4", "olivedrab4", "violetred", "darkgoldenrod1", "purple4"),
  breakNum = 15,
  memo = NULL,
  outpath = getwd(),
  test.method = "auto",
  file.type = "pdf",
  file.output = TRUE,
  dpi = 300
)

Arguments

phe	phenotype data
col	The color vector of the histogram. If the number of colors is less than break.n, the color will be reused. If the number of colors is greater than break.n, only the previous break.n colors will be used.
breakNum	the number of cells for the histogram. The default value is 15.
memo	Character. A text marker on output files
outpath	Effective only when file.output = TRUE, determines the path of the output file
test.method	The method used to test the normal distribution. The options are "auto", "Shapiro-Wilk", "Kolmogorov-Smirnov", and NULL. When set to "auto", "Shapiro- Wilk" method, "Kolmogorov-Smirnov" method will be used when it is greater than 5000, and it will not be tested when set to NULL.
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.
file.output	Logical value. If TRUE, the figures will be generated.
dpi	The resolution of the image, specifying how many pixels per inch.

Value

Output file: MVP.Phe_Distribution.<trait>.<type>

Examples

phePath <- system.file("extdata", "07_other", "mvp.phe", package = "rMVP")
phe <- read.table(phePath, header=TRUE)

MVP.Hist(phe, file.output = FALSE)

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