plot_gemini.R

#!/usr/bin/env Rscript
#
# Usage: plot_gemini.R <file.tsv>
#

my_required <- c('ggplot2', 'reshape2', 'ggthemes')
for (my_package in my_required){
   if(my_package %in% rownames(installed.packages()) == FALSE){
      stop(paste("Please install", my_package, "first")) 
   }
}

library(ggplot2)
library(reshape2)
library(ggthemes)

args <- commandArgs(TRUE)
if (length(args) != 1){
  stop('Please provide input file')
}

my_file <- args[1]
my_pdf <- gsub(pattern = 'tsv', replacement = 'pdf', x = my_file)

df <- read.table(my_file, header = TRUE, stringsAsFactors = FALSE)
names(df) <- c('foobar', 'Count')
df$foobar <- factor(df$foobar, levels = df$foobar)

df_melt <- melt(df)

my_plot <- ggplot(df_melt, aes(x = foobar, y = value, fill = foobar, label = value)) +
                  geom_bar(stat = "identity") +
                  theme(axis.title.x = element_blank(),
                        axis.text.x = element_blank(),
                        axis.ticks.x = element_blank(),
                        legend.title = element_blank()) +
                  labs(y = 'Count', x = element_blank()) +
                  theme_hc() +
                  geom_text()

ggsave(filename = my_pdf, plot = my_plot, dpi = 150, width = 30, height = 20, units = 'cm')