Skill: GWAS Circos Plot (R)
Category
Omics
When to Use
The visualization of Genome-Wide Association Study (GWAS) results mainly includes SNP circular plots displayed by chromosome positions, SNP density plots, Manhattan plots for significance screening, QQ plots comparing the distribution of observed p-values with expected p-values, etc., which are used to screen candidate variant genes at the genome-wide level.
Required R Packages
- CMplot
Minimal Reproducible Code
# Load packages
library(CMplot)
# Prepare data
# Example data
data(pig60K)
data <- pig60K
# Data preview
head(data, 5)
# Create visualization
# SNP screening genome circular map
CMplot(
data,
type = "p",
plot.type = "c",
chr.labels = paste("Chr", c(1:18, "X", "Y"), sep = ""),
r = 8,
cir.axis = TRUE,
outward = TRUE,
cir.axis.col = "black",
cir.chr.h = 2,
chr.den.col = "black",
file.output = FALSE,
verbose = FALSE,
mar = c(0,0,0,0)
)
Key Parameters
fill: Maps a variable to fill color for group comparisoncolor: Maps a variable to outline/point color
Tips
- Adjust text size with
theme(text = element_text(size = 14))for presentations - Include appropriate statistical thresholds (e.g., FDR < 0.05, |log2FC| > 1) in the visualization
- See the full tutorial for additional customization options and advanced examples