Package update

.gitignore

@@ -11,3 +11,4 @@
 .Rproj.user/F9589ABC/saved_source_markers
 .Rproj.user
 .Rbuildignore
+inst/doc

DESCRIPTION

@@ -3,13 +3,18 @@ Type: Package
 Title: Repeated Evolution in Cancer (REVOLVER)
 Version: 0.1.0
 Author: Giulio Caravagna
-Authors@R: person("Giulio", "Caravagna", role = c("aut", "cre"), email = "[email protected]")
+Authors@R: c(
+    person("Giulio", "Caravagna", email = "[email protected]", c("aut", "cre")),
+    person("Ylenia", "Giarratano", email = "[email protected]", role = "ctb"),
+    person("Daniele", "Ramazzotti", email = "[email protected]", role = "ctb"))
 Maintainer: Giulio Caravagna <[email protected]>
 Description: The R package that implements the REVOLVER algorithm to compute Repeated Evolution in Cancer from multi-region sequencing data.
 License: GPL
 Encoding: UTF-8
 LazyData: true
 Imports: crayon, RColorBrewer, purrr, cluster, igraph, pheatmap, TRONCO, parallel, doParallel, matrixcalc, entropy, matrixStats, gridExtra, Rgraphviz, qualvar, vegan, xlsx, rJava
 RoxygenNote: 6.0.1
-
-
+Suggests: 
+    knitr,
+    rmarkdown
+VignetteBuilder: knitr

R/rev_cohort.R

@@ -130,9 +130,11 @@ print.rev_cohort <- function(x, digits = max(3, getOption("digits") - 3), ...)
 
     cat(cyan('\n\tTL Model Fit  :'), ifelse(is.null(x$fit), red('NO\n'), green('YES ')), '\n')
 
+    longest.name = max(nchar(names(x$phylogenies)))
+
     patf = function(w, fit){
       s = paste(
-        yellow(sprintf('%15s', names(x$phylogenies)[w])),  ': ',
+        yellow(sprintf(paste('%', longest.name, 's', sep = ''), names(x$phylogenies)[w])),  ': ',
           sprintf('k = %3s | t = %3s | n = %2s | r = %2s | m = %4s | d = %2s',
                   length(x$phylogenies[[w]]),
                   rev_count_information_transfer_comb(x, names(x$phylogenies)[w]),