subScriptPlotting

#!/usr/bin/env Rscript 
# Embedded R script for domain plotting

pdf(NULL)
args <- commandArgs(TRUE)
TABLE <- args[1]
OUTPLOT <- args[2]
if (!isTRUE(suppressMessages(suppressWarnings(require(ggplot2))))) {
  stop("The package 'ggplot2' was not found, plotting will not be performed. You can use the DomainCoordinates.txt file to plot externally", call. = F)
}
if (!isTRUE(suppressMessages(suppressWarnings(require(dplyr))))) {
  stop("The package 'dplyr' was not found, plotting will not be performed. You can use the DomainCoordinates.txt file to plot externally", call. = F)
}
tabella <- read.delim(TABLE, sep = '\t', header = T)

if (nrow(tabella) == 0){
  stop("No Domains found in supplied fasta.", call. = F)
}

tabella %>% 
  distinct() %>% 
  mutate(Start = as.numeric(as.character(Start)),
         End = as.numeric(as.character(End)),
         geneLength = as.numeric(as.character(geneLength)),
         MidPoint = (Start+End)/2) %>% 
  ggplot()+
  geom_segment(aes(y=geneName, yend = geneName,
                   x=1 , xend = geneLength))+
  geom_rect(aes(xmin = Start, xmax = End,
                ymin = as.numeric(geneName)-0.2, ymax = as.numeric(geneName)+0.2,
                fill = Domain),
            color = 'black')+
  geom_text(aes(y=geneName, x = MidPoint, label = Domain), 
            size = 4,
            position=position_jitter(width=0,height=0))+
  theme_minimal()+
  theme(panel.grid = element_blank(),
        axis.text = element_text(color = 'black'))+
  labs(y = '',
       x = '') +
  theme(legend.position="none",
        axis.text.y = element_text(size = 10),
  )
Hplot <- nrow(tabella)*0.1
Hplot <- ifelse(Hplot <= 30, 30, Hplot)
suppressMessages(suppressWarnings(ggsave(OUTPLOT, width = 30, height = Hplot, limitsize = FALSE)))