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<code>
#setwd("C:\\work\\script_test\\R\\diff_valcano")
#Args <- commandArgs()
path = "P30_vs_MV4_11.genes.DEA.xls"
title = "Difference expression genes of P30_vs_MV4_11"
savefile = "P30_vs_MV4_11.Dynamic_volcano_plot.html"
library(ggplot2)
library(plotly)
options(stringsAsFactors=FALSE)
data <- read.csv(path, header=TRUE, sep = "\t", quote = "")
#data <- read.csv(Args[1], header=TRUE, sep = "\t")

data_plot = data[!is.na(data[,4]),c(8, 4, 6)]
data_plot$change <-  as.factor(ifelse(data_plot$padjust < 0.005 & abs(data_plot$log2foldchange) > 1,ifelse(data_plot$log2foldchange > 1,'UP','DOWN'),'NOT'))

data_plot$sign <- ifelse(data_plot$padjust < 0.005 & abs(data_plot$log2foldchange) > 1,data_plot$gene_name,NA)
p <- ggplot(data = data_plot, aes(x = log2foldchange, y = -log10(padjust), color = change)) +
  geom_point(aes(text = sign), alpha=0.8, size = 0.8) +
  theme_bw(base_size = 15) +
  #labs(title = paste0("Difference expression of ", Args[2])) +
  labs(title = title) +
  theme(
    panel.grid.minor = element_blank(),
    panel.grid.major = element_blank(),
    plot.title = element_text(hjust = 0.5)) +
  scale_color_manual(name = "", values = c("red", "green", "black"), limits = c("UP", "DOWN", "NOT"))

p <- ggplotly(p)
#htmlwidgets::saveWidget(as_widget(p), paste0(Args[2], ".Dynamic_volcano_plot.html"))
htmlwidgets::saveWidget(as_widget(p), savefile)
</code>

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