hapVsPhenos {geneHapR}

hapVsPhenos

Description

hapVsPhenos

Usage

hapVsPhenos(
  hap,
  pheno,
  outPutSingleFile = TRUE,
  hapPrefix = "H",
  title = "Seita.0G000000",
  width = 12,
  height = 8,
  res = 300,
  compression = "lzw",
  filename.prefix = filename.prefix,
  filename.surfix = "pdf",
  filename.sep = "_",
  outlier.rm = TRUE,
  mergeFigs = TRUE,
  ...
)

Arguments

hap

object of hapResult class, generate withvcf2hap() or seqs2hap()

pheno

object of data.frame class, imported by import_pheno()

outPutSingleFile

TRUE or FALSE indicate whether put all figs into to each pages of single file or generate multi-files. Only worked while file type is pdf

hapPrefix

prefix of hapotypes, default as "H"

title

a charater which will used for figure title

width

manual option for determining the output file width in inches. (default: 12)

height

manual option for determining the output file height in inches. (default: 8)

res

The nominal resolution in ppi which will be recorded in the bitmap file, if a positive integer. Also used for units other than the default, and to convert points to pixels

compression

the type of compression to be used.

filename.prefix, filename.surfix, filename.sep

if multi files generated, file names will be formed by prefix filename.prefix, a seperate charcter filename.sep, pheno name, a dot and surfix filename.surfix, and file type was decide by filename.surfix; if single file was generated, file name will be formed by prefix filename.prefix, a dot and surfix filename.surfix

outlier.rm

whether remove ouliers, default as TRUE

mergeFigs

bool type, indicate whether merge the heat map and box plot or not. Default as FALSE

...

Arguments passed on to hapVsPheno

phenoName

pheno name for plot, should be one column name of pheno

minAcc,freq.min

If observations number of a Hap less than this number will not be compared with others or be ploted. Should not less than 3 due to the t-test will meaninglessly. Default as 5

angle

the angle of x labels

hjust,vjust

hjust and vjust of x labels

comparisons

a list contains comparison pairs eg. list(c("H001", "H002"), c("H001", "H004")), or a character vector contains haplotype names for comparison, or "none" indicates do not add comparisons.

method

a character string indicating which method to be used for comparing means.

method.args

a list of additional arguments used for the test method. For example one might use method.args = list(alternative = "greater") for wilcoxon test.

symnum.args

a list of arguments to pass to the function symnum for symbolic number coding of p-values. For example, symnum.args <- list(cutpoints = c(0, 0.0001, 0.001, 0.01, 0.05, Inf), symbols = c("****", "***", "**", "*", "ns")).

In other words, we use the following convention for symbols indicating statistical significance:

• ns: p > 0.05

• *: p <= 0.05

• **: p <= 0.01

• ***: p <= 0.001

• ****: p <= 0.0001

Value

No return value

Examples

data("geneHapR_test")

oriDir <- getwd()
temp_dir <- tempdir()
if(! dir.exists(temp_dir))
  dir.create(temp_dir)
setwd(temp_dir)
# analysis all pheno in the data.frame of pheno
hapVsPhenos(hapResult,
            pheno,
            outPutSingleFile = TRUE,
            hapPrefix = "H",
            title = "Seita.0G000000",
            filename.prefix = "test",
            width = 12,
            height = 8,
            res = 300)
setwd(oriDir)