comparison signature.r @ 2:dc862983eb98 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6806c0677e53d52164707faeb36947987f5c500a

1:ca2b04cdbf4d

## Setup R error handling to go to stderr
options(show.error.messages = F,
        error = function() {
            cat(geterrmessage(), file = stderr())
            q("no", 1, F)
        }
)
warnings()

library(RColorBrewer)

    make_option("--pdf", type = "character", help = "path to the pdf file with plots"),
    make_option("--title", type = "character", help = "Graph Title")
    )
parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
args <- parse_args(parser)
 
# data frames implementation
h_dataframe <- read.delim(args$h_dataframe, header = F)
colnames(h_dataframe) <- c("chrom", "overlap", "sig", "z-score")
h_dataframe$sig <- h_dataframe$sig * 100  # to get probs in %
z_dataframe <- read.delim(args$z_dataframe, header = F)
colnames(z_dataframe) <- c("chrom", "overlap", "sig", "z-score")

# functions
    globalgraph <- function() {
        pdf(args$pdf)

                   main = args$title,
                   par.strip.text = list(cex = .5),
                   pch = 19, lwd = 2,
                   as.table = TRUE,
                   layout = c(2, 12),
                   newpage = T,
                   ...)
           plot(p)
           dev.off()
    }

2:dc862983eb98

## Setup R error handling to go to stderr
options(show.error.messages = FALSE,
        error = function() {
            cat(geterrmessage(), file = stderr())
            q("no", 1, FALSE)
        }
)
warnings()

library(RColorBrewer)

    make_option("--pdf", type = "character", help = "path to the pdf file with plots"),
    make_option("--title", type = "character", help = "Graph Title")
    )
parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
args <- parse_args(parser)

# data frames implementation
h_dataframe <- read.delim(args$h_dataframe, header = FALSE)
colnames(h_dataframe) <- c("chrom", "overlap", "sig", "z-score")
h_dataframe$sig <- h_dataframe$sig * 100  # to get probs in %
z_dataframe <- read.delim(args$z_dataframe, header = FALSE)
colnames(z_dataframe) <- c("chrom", "overlap", "sig", "z-score")

# functions
    globalgraph <- function() {
        pdf(args$pdf)

                   main = args$title,
                   par.strip.text = list(cex = .5),
                   pch = 19, lwd = 2,
                   as.table = TRUE,
                   layout = c(2, 12),
                   newpage = TRUE,
                   ...)
           plot(p)
           dev.off()
    }