Gene Ranking Dotplot

Gene expression ranking visualization.

Setup

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

• Programming language: R

• Dependent packages: ggrepel; ggplot2; RColorBrewer

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

# Load packages
library(ggrepel)
library(ggplot2)
library(RColorBrewer)

Data Preparation

# Load data
data <- read.delim("files/Hiplot/061-gene-rank-data.txt", header = T)

# Convert data structure
## ordered by log2FoldChange and pvalue
data <- data[order(-data$log2FC, data$pvalue), ]
## add the rank column
data$rank <- 1:nrow(data)
## get the top n up and down gene for labeling
top_n <- 5
top_n_up <- rownames(head(data, top_n))
top_n_down <- rownames(tail(data, top_n))
genes_to_label <- c(top_n_up, top_n_down)
data2 <- data[genes_to_label, ]


# View data
head(data)

        gene   log2FC       pvalue rank
514 LOC91370 3.889820 8.478310e-03    1
293   LRRC25 3.492413 5.000000e-05    2
470   BEGAIN 3.312996 3.347634e-03    3
159   RDM1P5 3.125070 1.538852e-02    4
194    CLDN1 3.096516 2.622163e-02    5
626    KCNS1 2.949729 2.770000e-09    6

Visualization

# Gene Ranking Dotplot
p <- 
  ggplot(data, aes(rank, log2FC, color = pvalue, size = abs(log2FC))) + 
  geom_point() + 
  scale_color_gradientn(colours = colorRampPalette(brewer.pal(11,'RdYlBu'))(100)) +
  geom_hline(yintercept = c(-1, 1), linetype = 2, size = 0.3) +
  geom_hline(yintercept = 0, linetype = 1, size = 0.5) +
  geom_vline(xintercept = median(data$rank), linetype = 2, size = 0.3) + 
  geom_text_repel(data = data2, aes(rank, log2FC, label = gene),
                  size = 3, color = "red") +
  xlab("") + ylab("") + 
  ylim(c(-max(abs(data$log2FC)), max(abs(data$log2FC)))) +
  labs(color = "Pvalue", size = "Log2FoldChange") +
  theme_bw(base_size = 12) +
  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: Gene Ranking Dotplot