PhenStat (version 2.6.0)

scatterplotSexGenotypeBatch: Method "scatterplotSexGenotypeBatch"

Description

Graph function for the phenotypic dataset. Creates a scatterplot split by sex, genotype and batch. refGenotype data points are shown in black and the testGenotype data points are shown in red. Note: the batches are not ordered with time but allow assessment of how the testGenotype data lie relative to the variation within the refGenotype data.

Usage

scatterplotSexGenotypeBatch(phenList,depVariable=NULL,graphingName=NULL,outputMessages=TRUE)

Arguments

phenList

instance of the PhenList class; mandatory argument

depVariable

a character string defining the dependent variable of interest; mandatory argument

graphingName

a character string defining the name to be used on the graph for the dependent variable; mandatory argument

outputMessages

flag: "FALSE" value to suppress output messages; "TRUE" value to show output messages; default value TRUE

References

Karp N, Melvin D, Sanger Mouse Genetics Project, Mott R (2012): Robust and Sensitive Analysis of Mouse Knockout Phenotypes. PLoS ONE 7(12): e52410. doi:10.1371/journal.pone.0052410 West B, Welch K, Galecki A (2007): Linear Mixed Models: A practical guide using statistical software New York: Chapman & Hall/CRC 353 p.

See Also

PhenList

Examples

    file <- system.file("extdata", "test1.csv", package="PhenStat")
    test <- PhenList(dataset=read.csv(file),
            testGenotype="Sparc/Sparc")
    # box plot for dataset with two sexes: males and females
    scatterplotSexGenotypeBatch(test,
            depVariable="Bone.Mineral.Content",
            graphingName="BMC" )
    
    file <- system.file("extdata", "test4.csv", package="PhenStat")
    test_1sex <- PhenList(dataset=read.csv(file),
            testGenotype="Mysm1/+")
    # box plot for females only dataset
    scatterplotSexGenotypeBatch(test_1sex,depVariable="Lean.Mass", 
            graphingName="Lean Mass")