diff signature.r @ 2:dc862983eb98 draft

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

--- a/signature.r	Sat Oct 23 22:54:47 2021 +0000
+++ b/signature.r	Sat Oct 22 23:49:14 2022 +0000
@@ -1,8 +1,8 @@
 ## Setup R error handling to go to stderr
-options(show.error.messages = F,
+options(show.error.messages = FALSE,
         error = function() {
             cat(geterrmessage(), file = stderr())
-            q("no", 1, F)
+            q("no", 1, FALSE)
         }
 )
 warnings()
@@ -26,12 +26,12 @@
     )
 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
 args <- parse_args(parser)
- 
+
 # data frames implementation
-h_dataframe <- read.delim(args$h_dataframe, header = F)
+h_dataframe <- read.delim(args$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$z_dataframe, header = F)
+z_dataframe <- read.delim(args$z_dataframe, header = FALSE)
 colnames(z_dataframe) <- c("chrom", "overlap", "sig", "z-score")
 
 # functions
@@ -77,7 +77,7 @@
                    pch = 19, lwd = 2,
                    as.table = TRUE,
                    layout = c(2, 12),
-                   newpage = T,
+                   newpage = TRUE,
                    ...)
            plot(p)
            dev.off()