Three Genders

determineGenderYDom <- function(chromosone1,chromosone2)
{
    ## Function to determine the gender of a child based on the
    ## child's two chromosones.
    ##
    ## This assumes that Y is dominant with respect to both X and Z
    ##                   X is dominant with respect to Z

    if((chromosone1=="Y") | (chromosone2=="Y"))
    {
        return("M")
    }
    else if ((chromosone1=="X") | (chromosone2=="X"))
    {
        return("F")
    }
    return("V")
}

determineGenderZDom <- function(chromosone1,chromosone2)
{
    ## Function to determine the gender of a child based on the
    ## child's two chromosones.
    ##
    ## This assumes that Z is dominant with respect to both X and Y
    ##                   Y is dominant with respect to X

    if((chromosone1=="Z") | (chromosone2=="Z"))
    {
        return("V")
    }
    else if ((chromosone1=="Y") | (chromosone2=="Y"))
    {
        return("M")
    }
    return("F")
}



## Change the right hand of this assignment to change the way the
## script calculates dominance. The right hand side should be one of
## the functions above.
determineGender <- determineGenderZDom

addGenders <- function(leftChromosone1, leftChromosone2,    # chromosones of parent 1
                       rightChromosone1,rightChromosone2)   # chromosones of parent 2
{
    ## Function to determine the chromosones and genders of all possible
    ## children based on the chromosones of both parents.
    if(determineGender(leftChromosone1,leftChromosone2) !=
       determineGender(rightChromosone1,rightChromosone2))
    {
        ## The parents are of two different genders. Assume that they
        ## can have offspring. Return all possible permutations and
        ## the gender for each permutation.
        return(data.frame(
            chromosone1=c(leftChromosone1,leftChromosone2,leftChromosone1,leftChromosone2),
            chromosone2=c(rightChromosone1,rightChromosone2,rightChromosone2,rightChromosone1),
            gender=c(determineGender(leftChromosone1,rightChromosone1),
                     determineGender(leftChromosone2,rightChromosone2),
                     determineGender(leftChromosone1,rightChromosone2),
                     determineGender(leftChromosone2,rightChromosone1))))
    }
    return(NA)
}


## Define the possible chromosones
chromosones = c("X","Y","Z")

## Define an empty data frame that will contain all the possible children.
gender = data.frame(chromosone1=character(0),chromosone1=character(0),gender=character(0))


## Loop through all possible permutations for parent 1.
for (leftChromosone1 in chromosones)
{
    for (leftChromosone2 in chromosones)
    {
        if((leftChromosone1!="Y") || (leftChromosone2!="Y"))
        {
            ## Assume up front that there are no YY males. This
            ## assumes no males give birth.

            ## Now loop through all possible permutations for parent 2.
            for (rightChromosone1 in chromosones)
            {
                for (rightChromosone2 in chromosones)
                {
                    if((rightChromosone1!="Y") || (rightChromosone2!="Y"))
                    {
                        ## Assume up front that there are no YY males. This
                        ## assumes no males give birth.

                        babies <- addGenders(leftChromosone1, leftChromosone2,
                                             rightChromosone1,rightChromosone2)
                        if(length(babies)>1)
                        {
                            gender <- rbind(gender,babies)
                        }

                    }
                }
            }
        }
    }
}
## At this point we have a data frame which has the permutations for
## children assuming that males cannot give birth. The data frame also
## has the gender of each child, and it assumes that all combinations
## are equally likely.


if (length(gender$gender[(gender$chromosone1 == "Y") & (gender$chromosone2 == "Y")])>0)
{
    ## uh-oh.... it is possible to get YY males with this
    ## ordering. Need to go back and add those possibilities

    for (rightChromosone1 in chromosones)
    {
        for (rightChromosone2 in chromosones)
        {

            ## Add the possibilities when parent 1 is a YY diploid.
            babies <- addGenders("Y","Y",rightChromosone1,rightChromosone2)
            if(length(babies)>1)
            {
                gender <- rbind(gender,babies)
            }

            if((rightChromosone1!="Y") || (rightChromosone2!="Y"))
            {
                ## If the chromosones are not both Y then gotta add
                ## them when parent 2 is both.
                babies <- addGenders(rightChromosone1,rightChromosone2,"Y","Y")
                if(length(babies)>1)
                {
                    gender <- rbind(gender,babies)
                }

            }
        }
    }


}

gender$chromosone1 = as.factor(gender$chromosone1) # convert everything to factors
gender$chromosone2 = as.factor(gender$chromosone2)
gender$gender      = as.factor(gender$gender)

print(table(gender$gender))
plot(gender$gender)

children <- table(gender$chromosone1,gender$chromosone2)
print(children)
mosaicplot(children)