Remove duplicated scripts

biopet-core/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotScatter.R

-library(reshape2)
-library(ggplot2)
-library(argparse)
-
-parser <- ArgumentParser(description='Process some integers')
-parser$add_argument('--input', dest='input', type='character', help='Input tsv file', required=TRUE)
-parser$add_argument('--output', dest='output', type='character', help='Output png file', required=TRUE)
-parser$add_argument('--width', dest='width', type='integer', default = 500)
-parser$add_argument('--height', dest='height', type='integer', default = 500)
-parser$add_argument('--xlabel', dest='xlabel', type='character')
-parser$add_argument('--ylabel', dest='ylabel', type='character', required=TRUE)
-parser$add_argument('--llabel', dest='llabel', type='character')
-parser$add_argument('--title', dest='title', type='character')
-parser$add_argument('--removeZero', dest='removeZero', type='character', default="false")
-
-arguments <- parser$parse_args()
-
-png(filename = arguments$output, width = arguments$width, height = arguments$height)
-
-DF <- read.table(arguments$input, header=TRUE)
-
-if (is.null(arguments$xlabel)) xlab <- colnames(DF)[1] else xlab <- arguments$xlabel
-
-colnames(DF)[1] <- "Rank"
-
-DF1 <- melt(DF, id.var="Rank")
-
-if (arguments$removeZero == "true") DF1 <- DF1[DF1$value > 0, ]
-if (arguments$removeZero == "true") print("Removed 0 values")
-
-ggplot(DF1, aes(x = Rank, y = value, group = variable, color = variable)) +
-  xlab(xlab) +
-  ylab(arguments$ylabel) +
-  guides(fill=guide_legend(title=arguments$llabel)) +
-  theme(axis.text.x = element_text(angle = 90, hjust = 1, size = 8)) +
-  ggtitle(arguments$title) +
-  theme_bw() +
-  geom_point()
-
-dev.off()

biopet-core/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotXY.R

-library(reshape2)
-library(ggplot2)
-library(argparse)
-
-parser <- ArgumentParser(description='Process some integers')
-parser$add_argument('--input', dest='input', type='character', help='Input tsv file', required=TRUE)
-parser$add_argument('--output', dest='output', type='character', help='Output png file', required=TRUE)
-parser$add_argument('--width', dest='width', type='integer', default = 500)
-parser$add_argument('--height', dest='height', type='integer', default = 500)
-parser$add_argument('--xlabel', dest='xlabel', type='character')
-parser$add_argument('--ylabel', dest='ylabel', type='character', required=TRUE)
-parser$add_argument('--llabel', dest='llabel', type='character')
-parser$add_argument('--title', dest='title', type='character')
-parser$add_argument('--removeZero', dest='removeZero', type='character', default="false")
-
-arguments <- parser$parse_args()
-
-png(filename = arguments$output, width = arguments$width, height = arguments$height)
-
-DF <- read.table(arguments$input, header=TRUE)
-
-if (is.null(arguments$xlabel)) xlab <- colnames(DF)[1] else xlab <- arguments$xlabel
-
-colnames(DF)[1] <- "Rank"
-
-DF1 <- melt(DF, id.var="Rank")
-
-if (arguments$removeZero == "true") DF1 <- DF1[DF1$value > 0, ]
-if (arguments$removeZero == "true") print("Removed 0 values")
-
-ggplot(DF1, aes(x = Rank, y = value, group = variable, color = variable)) +
-  xlab(xlab) +
-  ylab(arguments$ylabel) +
-  guides(fill=guide_legend(title=arguments$llabel)) +
-  theme(axis.text.x = element_text(angle = 90, hjust = 1, size = 8)) +
-  ggtitle(arguments$title) +
-  theme_bw() +
-  geom_line()
-
-dev.off()

biopet-core/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/stackedBar.R

-library(reshape2)
-library(ggplot2)
-library(argparse)
-
-parser <- ArgumentParser(description='Process some integers')
-parser$add_argument('--input', dest='input', type='character', help='Input tsv file', required=TRUE)
-parser$add_argument('--output', dest='output', type='character', help='Output png file', required=TRUE)
-parser$add_argument('--width', dest='width', type='integer', default = 500)
-parser$add_argument('--height', dest='height', type='integer', default = 500)
-parser$add_argument('--xlabel', dest='xlabel', type='character')
-parser$add_argument('--ylabel', dest='ylabel', type='character', required=TRUE)
-parser$add_argument('--llabel', dest='llabel', type='character')
-parser$add_argument('--title', dest='title', type='character')
-
-arguments <- parser$parse_args()
-
-png(filename = arguments$output, width = arguments$width, height = arguments$height)
-
-DF <- read.table(arguments$input, header=TRUE)
-
-if (is.null(arguments$xlabel)) xlab <- colnames(DF)[1] else xlab <- arguments$xlabel
-
-colnames(DF)[1] <- "Rank"
-
-DF1 <- melt(DF, id.var="Rank")
-
-ggplot(DF1, aes(x = Rank, y = value, fill = variable)) + 
-  xlab(xlab) +
-  ylab(arguments$ylabel) + 
-  guides(fill=guide_legend(title=arguments$llabel)) +
-  theme(axis.text.x = element_text(angle = 90, hjust = 1, size = 8)) +
-  geom_bar(stat = "identity", width=1) +
-  ggtitle(arguments$title)
-
-dev.off()