GOBubble Plot

The gobubble plot is used to display Z-score coloured bubble plot of terms ordered alternatively by z-score or the negative logarithm of the adjusted p-value.

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/078-gobubble-data.txt", header = T)

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

# 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

# GOBubble Plot
p <- function () {
  GOBubble(data, display = "single", title = "GO Enrichment Bubbleplot",
           colour = c("#FC8D59","#FFFFBF","#99D594"),
           labels = 0,  ID = T, table.legend = T, table.col = T, bg.col = F) + 
  theme(plot.title = element_text(hjust = 0.5))
}
p <- as.ggplot(p)

p

Figure 1: GOBubble Plot

As shown in the example figure, the x- axis of the plot represents the z-score. The negative logarithm of the adjusted p-value (corresponding to the significance of the term) is displayed on the y-axis. The area of the plotted circles is proportional to the number of genes assigned to the term. Each circle is coloured according to its category and labeled alternatively with the ID or term name.