File:Genotype phenotype regression.svg
Summary
| Description |
English: Illustration of an association between phenotype and genotype. Data is simulated, actual associations detected in GWAS are usually much smaller. Fitted regression line shown in red and actual phenotype means for each genotype are shown in blue crosses. |
| Date | |
| Source | Own work |
| Author | D Wells |
| SVG development | Category:Valid SVG created with R code#Genotype%20phenotype%20regression.svg  The file size of this SVG plot may be irrationally large because its text has been converted to paths inhibiting translations. |
| Source code | R codelibrary(ggplot2)
set.seed(5678)
n = 1000
allele_freq = 0.3
genotypes = rbinom(n, size = 2, p = allele_freq) # assuming HWE
mean_phenotype = function(genotype) 0.1 + 0.3 * genotype
phenotypes = rnorm(n, mean_phenotype(genotypes))
svg("genotype_phenotype_regression.svg", width=4, height=4)
ggplot(data.frame(phenotypes, genotypes), aes(genotypes, phenotypes)) +
geom_jitter(alpha=0.2, width=0.3) +
geom_smooth(method="lm", colour="red3", fullrange=T, se=F) +
stat_summary(fun = mean, geom="point", shape="+", size=7, colour="blue3") +
scale_x_continuous(breaks=c(0, 1, 2), labels=c("0 (CC)","1 (CT)","2 (TT)"), limits=c(-1,3)) +
coord_cartesian(xlim=c(-0.5, 2.5))+
theme_classic() +
xlab("Number of T alleles") + ylab("Phenotype")
dev.off()
|
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