qtl (version 1.01-9)

effectplot: Plot phenotype means against genotypes at one or two markers.

Description

Plot the phenotype means for each group defined by the genotypes at one or two markers (or the values at a discrete covariate).

Usage

effectplot(cross, pheno.col=1, mname1, mark1, geno1, mname2, mark2,
           geno2, main, ylim, add.legend=TRUE, draw=TRUE,
           var.flag=c("pooled","group"))

Arguments

cross

An object of class cross.

pheno.col

Column number in the phenotype matrix which to be drawn in the plot.

mname1

Name for the first marker.

mark1

Genotype data for the first marker. If unspecified, genotypes will be taken from the data in the input cross object, using the name specified in mname1.

geno1

Names for the genotypes (or classes in a covariate).

mname2

Name for the second marker (optional).

mark2

Like mark1 (optional).

geno2

Names for the genotypes (or classes in a covariate).

main

Optional figure title.

ylim

Y-axis limits.

add.legend

A logical value to indicate add legend or not.

draw

A logical value to indicate generate the plot or not. If FALSE, no figure will be plot and this function can be used to calculate the group means and standard errors.

var.flag

The method to calculate the group variance. "pooled" means to use the pooled variance and "group" means to calculate from individual group.

Value

• A data.frame containing the phenotype means and standard deviations for each group.

Details

In the plot, the Y-axis is the phenotype. X-axis is the genotype for the first marker. In the case of one marker, there will be one line in the figure. In the case of two markers, the x-axis is for different genotypes of the second marker, and the first marker is represented by lines in different colors. Error bars are plotted at $\pm$ 1 SE.

See Also

plot.pxg, find.marker, effectscan

Examples

data(fake.f2)
fake.f2 <- subset(fake.f2, chr=c(1, 13, "X"))

# impute gneotype data
fake.f2.impute <- sim.geno(fake.f2, step=5, n.draws=64)fake.f2.impute <- sim.geno(fake.f2, step=5, n.draws=8)

########################################
# one marker plots
########################################
### plot of genotype-specific phenotype means for 1 marker
mname <- find.marker(fake.f2, 1, 37) # marker D1M437
effectplot(fake.f2, pheno.col=1, mname1=mname)

### plot a pseudomarker
effectplot(fake.f2.impute, pheno.col=1, mname1=mname)

### plot a phenotype
# Plot of sex-specific phenotype means,
# note that "sex" must be a phenotype name here
effectplot(fake.f2, mname1="sex", geno1=c("F","M"))
# alternatively I can do it this way
sex <- fake.f2$pheno[,2]
effectplot(fake.f2, mname1="Sex", mark1=sex, geno1=c("F","M"))

########################################
# two markers plots
########################################

### plot two markers
# plot of genotype-specific phenotype means for 2 markers
mname1 <- find.marker(fake.f2, 1, 37) # marker D1M437
mname2 <- find.marker(fake.f2, 13, 24) # marker D13M254
effectplot(fake.f2, mname1=mname1, mname2=mname2)

### plot two pseudomarkers
pmname1 <- "c1.loc35"
pmname2 <- "c13.loc25"
effectplot(fake.f2.impute, mname1=pmname1, mname2=pmname2)

### plot one marker and one imputed pseudomarker
mark1 <- fake.f2.impute$geno[[1]]$draws[,11,]
effectplot(fake.f2, mname1="D1M437", mark1=mark1, mname2="D13M254")

### Plot of sex- and genotype-specific phenotype means 
mname <- find.marker(fake.f2, 13, 24) # marker D13M254
# sex and a marker
effectplot(fake.f2, mname1=mname, mname2="Sex",
           mark2=fake.f2$pheno$sex, geno2=c("F","M"))
# sex and a pseudomarker
effectplot(fake.f2.impute, mname1=mname, mname2="Sex",
           mark2=fake.f2$pheno$sex, geno2=c("F","M"))

# Same as above, switch role of sex and the marker
# sex and marker
effectplot(fake.f2, mname1="Sex", mark1=fake.f2$pheno$sex,
           geno1=c("F","M"), mname2=mname)
# sex and pseudomarker
effectplot(fake.f2.impute, mname1="Sex", mark1=fake.f2$pheno$sex,
           geno1=c("F","M"), mname2=mname)

# X chromosome marker
mname <- find.marker(fake.f2, "X", 14) # marker DXM66
effectplot(fake.f2, mname1=mname)

# Two markers, including one on the X
mname1 <- find.marker(fake.f2, 13, 24) # marker D13M254
mname2 <- find.marker(fake.f2, "X", 14) # marker DXM66
effectplot(fake.f2, mname1=mname1, mname2=mname2)