Suggests dependencies + Documentation

DESCRIPTION

@@ -11,7 +11,7 @@ Description: clonevol performs clonal ordering and visualization using
     (sum and cross rules), hence it tolerates error and variability
     in cellular prevalence estimates of individual variants.
 Depends: R (>= 2.1.5)
-Imports: stats, ggplot2
+Imports: stats, graphics, grDevices, utils, methods, base, ggplot2
 License: GNU General Public License v3.0
 LazyData: true
 Suggests: knitr, rmarkdown, grid, gridBase, gridExtra, ggplot2, reshape2,

NAMESPACE

@@ -13,3 +13,4 @@ export(plot.tree.clone.as.branch)
 export(plot.variant.clusters)
 export(transfer.events.to.consensus.trees)
 export(variant.box.plot)
+import(ggplot2)

R/boxplot.r

@@ -256,7 +256,7 @@ variant.box.plot <- function(...){
 #' @param ccf Plot CCF (calculated as 2xVAF) instead of VAF (default=FALSE)
 #' @param founding.cluster Founding cluster (default=NULL)
 #' @param show.cluster.label Show cluster label in axis (default=TRUE)
-#'
+#' @import ggplot2
 #' @export plot.variant.clusters
 #' @examples
 #' data(aml1)
@@ -795,6 +795,7 @@ plot.variant.clusters <- function(df,
 #' @param height Height of the output file
 #' @param out.file Output file (can be pdf, png, etc.) (default=NULL). If equal
 #' NULL, this function return the plot that can be print
+#' @import ggplot2
 #' @export plot.cluster.flow
 #' @examples
 #' data(aml1)
@@ -920,6 +921,7 @@ plot.cluster.flow <- function(variants,
 #' @param xMinSmall,xMaxSmall Min and max values for the x axis in single-page plot (default=0,70)
 #' @param yMinSmall,yMaxSmall Min and max values for the y axis in single-page plot (default=0,70)
 #' @param out.prefix Output files' prefix
+#' @import ggplot2
 #' @export plot.pairwise
 #' @examples
 #' data(aml1)

R/clonevol.r

@@ -3683,7 +3683,10 @@ get.clonevol.colors <- function(num.colors, strong.color=F){
     }
 }
 
-
+#' Plot ClonEvol colors
+#' @description Plot ClonEvol colors
+#' @param num.colors Number of colors
+#' @import ggplot2
 plot.clonevol.colors <- function(num.colors=40){
     library(ggplot2)
     colors = get.clonevol.colors(num.colors)
@@ -3851,7 +3854,7 @@ generate.cloud.of.cells <- function(colors, maxiter=1000){
 #' the figure size is, the smaller this value needs to be (default = 0.1)
 #' @param clone.grouping: how the cells of the same clone being grouped
 #' values are c("random", "horizontal", "vertical"), default="random"
-#'
+#' @import ggplot2
 plot.cloud.of.cells <- function(cells, title='', alpha=1, frame=F,
     cell.border.color='black', cell.border.size=0.1,
     clone.grouping='random', limits=c(-50,50)){

man/compare.clone.trees.Rd

@@ -4,7 +4,7 @@
 \alias{compare.clone.trees}
 \title{Compare two clonal evolution trees}
 \usage{
-\method{compare}{clone.trees}(v1, v2, compare.seeding.models = T)
+compare.clone.trees(v1, v2, compare.seeding.models = T)
 }
 \arguments{
 \item{v1:}{clonal evolution tree data frame 1}

man/compare.clone.trees.removing.leaves.Rd

@@ -4,7 +4,7 @@
 \alias{compare.clone.trees.removing.leaves}
 \title{Compare two merged clonal evolution trees}
 \usage{
-\method{compare}{clone.trees.removing.leaves}(v1, v2, ignore.seeding = F)
+compare.clone.trees.removing.leaves(v1, v2, ignore.seeding = F)
 }
 \arguments{
 \item{v1:}{clonal evolution tree data frame 1}

man/plot.clonevol.colors.Rd

@@ -0,0 +1,15 @@
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/clonevol.r
+\name{plot.clonevol.colors}
+\alias{plot.clonevol.colors}
+\title{Plot ClonEvol colors}
+\usage{
+\method{plot}{clonevol.colors}(num.colors = 40)
+}
+\arguments{
+\item{num.colors}{Number of colors}
+}
+\description{
+Plot ClonEvol colors
+}
+

vignettes/clonevol.Rmd

@@ -66,7 +66,6 @@ install.packages('gridExtra')
 install.packages('ggplot2')
 install.packages('igraph')
 install.packages('packcircles')
-install_github('hdng/trees')
 ```
 
 **Install from Bioconductor**