Bubble

The bubble chart is a statistical chart that shows the third variable by the size of the bubble on the basis of the scatter chart, so that the three variables can be compared and analyzed simultaneously.

Setup

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

• Programming language: R

• Dependent packages: ggplot2; stringr

# Install packages
if (!requireNamespace("ggplot2", quietly = TRUE)) {
  install.packages("ggplot2")
}
if (!requireNamespace("stringr", quietly = TRUE)) {
  install.packages("stringr")
}

# Load packages
library(ggplot2)
library(stringr)

Data Preparation

The loaded data are GO Term,Gene Ridio, Gene count and P-value.

# Load data
data <- read.delim("files/Hiplot/016-bubble-data.txt", header = T)

# convert data structure
data[, 1] <- str_to_sentence(str_remove(data[, 1], pattern = "\\w+:\\d+\\W"))
topnum <- 7
data <- data[1:topnum, ]
data[, 1] <- factor(data[, 1], level = rev(unique(data[, 1])))

# View data
head(data)

                               Term Count     Ratio   PValue
1                   Immune response    20 10.471204 9.61e-08
2     Defense response to bacterium    11  5.759162 3.02e-06
3                   Cell chemotaxis     8  4.188482 5.14e-06
4                     Cell adhesion    17  8.900524 2.73e-05
5             Complement activation     8  4.188482 3.56e-05
6 Extracellular matrix organization    11  5.759162 4.23e-05

Visualization

# Bubble
p <- ggplot(data, aes(Ratio, Term)) +
  geom_point(aes(size = Count, colour = -log10(PValue))) +
  scale_colour_gradient(low = "#00438E", high = "#E43535") +
  labs(colour = "-log10 (PValue)", size = "Count", x = "Ratio", y = "Term", 
       title = "Bubble Plot") +
  scale_x_continuous(limits = c(0, max(data$Ratio) * 1.2)) +
  guides(color = guide_colorbar(order = 1), size = guide_legend(order = 2)) +
  scale_y_discrete(labels = function(x) {str_wrap(x, width = 65)}) +
  theme_bw() +
  theme(text = element_text(family = "Arial"),
        plot.title = element_text(size = 12,hjust = 0.5),
        axis.title = element_text(size = 12),
        axis.text = element_text(size = 10),
        axis.text.x = element_text(angle = 0, hjust = 0.5,vjust = 1),
        legend.position = "right",
        legend.direction = "vertical",
        legend.title = element_text(size = 10),
        legend.text = element_text(size = 10))

p

Figure 1: Bubble

The x-axis represents Gene Ridio, and the y-axis is GO Term; The size of the dot represents the number of genes, and the color of the dot represents the high or low P value.