File:Genotype phenotype regression.svg
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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 | The SVG code is valid. This plot was created with R. 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()
|
Licensing
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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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