• Packages may useful for visualization, ggplot2, lattice, and others
  • The grid system in R - draw any thing you want

  • Recreation of potentially useful figures

  • The overall apperence of the figure
library(ggplot2)
t <- theme_classic() + # Set to a white theme
  theme(axis.text = element_text( size = 16,family="Arial",color="black"), # x tick label and y tick label
        axis.title = element_text(size =18, face="bold",family="Arial",color="black"), # x label and y label
        legend.text = element_text( size = 14,family="Arial",color="black"),
        legend.title = element_text( size = 16,family="Arial",color="black"),
        axis.line = element_blank(), # remove x axis and y axis
        panel.background = element_rect(fill="#F5F5F5"), # Background color
        panel.border = element_rect(color="black",fill=NA,size=1) # border of the figure
  )  # Control details of the figures appearance
  • Scatter plot
g <- ggplot(iris, aes(x=Petal.Length, y=Sepal.Length,col=Species)) + 
  geom_point(size=2, shape=22) + # Size and Shape of the dot
  #scale_colour_viridis_d() + # Set color scale
  scale_color_manual(values=c("#104E8B","#BCD2EE","#70B5B3")) + 
  xlab("Petal") + # Change x title
  ylab("Sepal") + # Change y title
  t
  • Boxplot / Violin plot
g <- ggplot(iris, aes(x=Species, y=Sepal.Length,fill=Species)) + 
  geom_boxplot(width=0.4) + # Size and Shape of the dot
  # geom_violin() + 
  scale_fill_manual(values=c("#104E8B","#BCD2EE","#70B5B3")) + # Set color scale
  xlab("Petal") + # Change x title
  ylab("Sepal") + # Change y title
  t +
  theme(axis.text.x = element_text(angle = 45,hjust = 1) # x tick label and y tick label, right-horizonton alignment 
  )
  • Use grid package for more customized plots
    • ggplot2 , lattice are all based on grid grammer
    • We don’t need to implement plot function based on low level, but grid function can make it possible to control every single line and every single point in figure generated by ggplot2 like tools
    • See https://bookdown.org/rdpeng/RProgDA/the-grid-package.html
    • For ggplot2, type grid.force() and grid.ls(), we get the names of ggplot2 elements
    • Then their property can be edited like grid.edit(name, gp = gpar(col = "red"))
  • Heatmap
library(pheatmap)
library(pals)
# Generate a demo
exp.mat = matrix(rnorm(200), 20, 10)
exp.mat[1:10, seq(1, 10, 2)] = exp.mat[1:10, seq(1, 10, 2)] + 3
exp.mat[11:20, seq(2, 10, 2)] = exp.mat[11:20, seq(2, 10, 2)] + 2
exp.mat[15:20, seq(2, 10, 2)] = exp.mat[15:20, seq(2, 10, 2)] + 4
colnames(exp.mat) = paste("Sample", 1:10, sep = "")
rownames(exp.mat) = paste("Gene", 1:20, sep = "")
pheatmap(exp.mat,color = pals::coolwarm(100))