GOCircle Plot

Authors

[Editor] Hu Zheng;

[Contributors]

The gocircle plot is used to display the circular plot combines gene expression and gene- annotation enrichment data. A subset of terms is displayed like the GOBar plot in combination with a scatter plot of the gene expression data. The whole plot is drawn on a specific coordinate system to achieve the circular layout. The segments are labeled with the term ID.

Setup

  • System Requirements: Cross-platform (Linux/MacOS/Windows)

  • Programming language: R

  • Dependent packages: GOplot; ggplotify

# Install packages
if (!requireNamespace("GOplot", quietly = TRUE)) {
  install.packages("GOplot")
}
if (!requireNamespace("ggplotify", quietly = TRUE)) {
  install.packages("ggplotify")
}

# Load packages
library(GOplot)
library(ggplotify)

Data Preparation

The loaded data are the results of GO enrichment with seven columns: category, GO id, GO term, gene count, gene name, logFC, adjust pvalue and zscore.

# Load data
data <- read.delim("files/Hiplot/079-gocircle-data.txt", header = T)

# Convert data structure
colnames(data) <- c("category","ID","term","count","genes","logFC","adj_pval","zscore")
data <- data[!is.na(data$adj_pval),]
data$adj_pval <- as.numeric(data$adj_pval)
data$zscore <- as.numeric(data$zscore)
data$count <- as.numeric(data$count)

# View data
head(data)
  category         ID              term count  genes      logFC adj_pval
1       BP GO:0007507 heart development    54   DLC1 -0.9707875 2.17e-06
2       BP GO:0007507 heart development    54   NRP2 -1.5153173 2.17e-06
3       BP GO:0007507 heart development    54   NRP1 -1.1412315 2.17e-06
4       BP GO:0007507 heart development    54   EDN1  1.3813006 2.17e-06
5       BP GO:0007507 heart development    54 PDLIM3 -0.8876939 2.17e-06
6       BP GO:0007507 heart development    54   GJA1 -0.8179480 2.17e-06
      zscore
1 -0.8164966
2 -0.8164966
3 -0.8164966
4 -0.8164966
5 -0.8164966
6 -0.8164966

Visualization

# GOCircle Plot
p <- function () {
  GOCircle(data, title = "GO Enrichment Circleplot",
           nsub = 10, rad1 = 2, rad2 = 3, table.legend = T, label.size = 5,
           zsc.col = c("#FC8D59","#FFFFBF","#99D594")) + 
    theme(plot.title = element_text(hjust = 0.5))
}
p <- as.ggplot(p)

p
FigureΒ 1: GOCircle Plot

As shown in the example figure, the outer circle shows a scatter plot for each term of the logFC of the assigned genes. Red circles display up-regulation and blue ones down-regulation by default.