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Original file (SVG file, nominally 360 × 360 pixels, file size: 378 KB)
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 | |
| 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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File history
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| Date/Time | Thumbnail | Dimensions | User | Comment | |
|---|---|---|---|---|---|
| current | 22:58, 5 October 2021 | | 360 × 360 (378 KB) | D Wells | Uploaded own work with UploadWizard |
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