| effectplot {qtl} | R Documentation |
Plot the phenotype means for each group defined by the genotypes at one or two markers (or the values at a discrete covariate).
effectplot(cross, pheno.col=1, mname1, mark1, geno1, mname2, mark2,
geno2, main, ylim, add.legend=TRUE, draw=TRUE,
var.flag=c("pooled","group"))
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. |
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 +/- 1 SE.
A data.frame containing the phenotype means and standard deviations for each group.
Hao Wu, hao@jax.org; Karl W Broman, kbroman@jhsph.edu
plot.pxg, find.marker,
effectscan
data(fake.f2)
# impute gneotype data
## Not run:
fake.f2.impute <- sim.geno(fake.f2, step=5, n.draws=64)
## End(Not run)
########################################
# 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)