codes_for_plotting_in_r.txt

#######################################################################################
# Codes for plotting in R
library(ggplot2)

#### Part 1: GO term Biological process ####

# Set working directory for GO term Biological process
setwd("YOUR_PATH_HERE_GO_TERM")

# Load GO term Biological process data
go_dt <- read.csv("mRNA_TargetGene_GOBP02.csv", header=TRUE)

# Set levels for Groups factor
go_dt$Groups <- factor(go_dt$Groups, levels=c("3dpi", "7dpi", "21dpi"))

# Plotting GO term Biological process data
ggplot(go_dt, aes(Groups, KEGG_Pathways)) +
  geom_point(aes(size=GeneNum, color=Qvalue)) +
  theme_bw() +
  scale_color_gradient(low="#66FF33", high="#CC3300") +
  scale_size_continuous(range=c(1.5, 6)) +
  labs(x="Groups", y="GO-BP Terms") +
  theme(axis.text = element_text(color="black"),
        axis.title = element_text(face="bold"),
        legend.title = element_text(face="bold"),
        plot.margin = unit(rep(0.5, 4), "cm")) +
  scale_x_discrete(labels = c('3dpi', '7dpi', '21dpi'))

#### Part 2: KEGG Pathways ####

# Set working directory for KEGG
setwd("YOUR_PATH_HERE_KEGG")

# Load KEGG data
kegg_dt <- read.csv("miRNA_TargetGene_KEGG.csv", header=TRUE)

# Set levels for Groups factor
kegg_dt$Groups <- factor(kegg_dt$Groups, levels=c("3dpi", "7dpi", "21dpi"))

# Plotting KEGG data
ggplot(kegg_dt, aes(Groups, KEGG_Pathways)) +
  geom_point(aes(size=GeneNum, color=Qvalue)) +
  theme_bw() +
  scale_color_gradient(low="#FF3333", high="#0000CC") +
  scale_size_continuous(range=c(1.5, 6)) +
  labs(x="Groups", y="KEGG Pathways") +
  theme(axis.text = element_text(color="black"),
        axis.title = element_text(face="bold"),
        legend.title = element_text(face="bold"),
        plot.margin = unit(rep(0.5, 4), "cm")) +
  scale_x_discrete(labels = c('3dpi', '7dpi', '21dpi'))

#### Part 3: Volcano Plot ####

# Set working directory for Volcano plot
setwd("YOUR_PATH_HERE_VOLCANO")

# Load Volcano plot data
volcano_dt <- read.csv("21dpi.csv", header=TRUE, na.strings="#N/A")

# Plotting Volcano plot data
ggplot(volcano_dt, aes(x=Log2FC, y=-log10(Pvalue), colour=Trend)) +
  geom_point(alpha=0.75, size=3.5, shape=16) +
  scale_color_manual(values=c("#4393C3", "#d2dae2", "#D6604D")) +
  xlim(-10, 10) + ylim(-1, 320) +
  geom_vline(xintercept=c(-1, 1), lty=2, col="black", lwd=0.3) +
  geom_hline(yintercept=-log10(0.05), lty=2, col="black", lwd=0.3) +
  theme_bw() +
  labs(x="Log2(FoldChange)", y="-Log10(Qvalue)")