R/data.R

In amf71/cloneMap: A Package to Construct Visual Representations of the Spatial Distribution of Somatic Clones in a Tissue / Sample

#' The first example CCF table 
#'
#' A table specifying the Cancer cell fractions (CCFs) of clones
#' which you wish to plot
#'
#' @format A data frame with 4 rows and 2 variables:
#' \describe{
#'  \item{clones}{names of clones}
#'  \item{CCF}{the cancer cell fraction (CCF) of specified clones}
#' }
#'
'CCFs_example_1' 

#' The second example CCF table 
#'
#' A table specifying the Cancer cell fractions (CCFs) of clones
#' which you wish to plot
#'
#' @format A data frame with 10 rows and 2 variables:
#' \describe{
#'  \item{clones}{names of clones}
#'  \item{CCF}{the cancer cell fraction (CCF) of specified clones}
#' }
#'
'CCFs_example_2' 

#' The simple example CCF table 
#'
#' A table specifying the Cancer cell fractions (CCFs) of clones
#' which you wish to plot
#'
#' @format A data frame with 4 rows and 2 variables:
#' \describe{
#'  \item{clones}{names of clones}
#'  \item{CCF}{the cancer cell fraction (CCF) of specified clones}
#' }
#'
'CCFs_simple_example'

#' A example of input to specify clone colours
#'
#' A named vector of length 10 with clones indicated 
#' as names and content as colours
#'
'clone_colours_example'

#' The a phylogenetic tree with all subclones in CCF examples 1 & 2
#'
#' A table specifying phylogentic relationships between clones
#'
#' @format A data frame with 9 rows and 2 variables:
#' \describe{
#'  \item{parent}{name of parent clone}
#'  \item{daughter}{name of daughter clone}
#' }
#'
'tree_example'

#' The a phylogenetic tree with all subclones in CCF example 1
#'
#' A table specifying phylogentic relationships between clones
#'
#' @format A data frame with 8 rows and 2 variables:
#' \describe{
#'  \item{parent}{name of parent clone}
#'  \item{daughter}{name of daughter clone}
#' }
#'
'tree_example_1'

#' The a phylogenetic tree with all subclones in CCF example 2
#'
#' A table specifying phylogentic relationships between clones
#'
#' @format A data frame with 3 rows and 2 variables:
#' \describe{
#'  \item{parent}{name of parent clone}
#'  \item{daughter}{name of daughter clone}
#' }
#'
'tree_example_2'


#' The a phylogenetic tree with all subclones in a polyclonal CCF example
#'
#' A table specifying phylogentic relationships between clones
#'
#' @format A data frame with 3 rows and 2 variables:
#' \describe{
#'  \item{parent}{name of parent clone}
#'  \item{daughter}{name of daughter clone}
#' }
#'
'tree_example_poly'

#' A polyclonal example CCF table 
#'
#' A table specifying the Cancer cell fractions (CCFs) of clones
#' which you wish to plot
#'
#' @format A data frame with 4 rows and 2 variables:
#' \describe{
#'  \item{clones}{names of clones}
#'  \item{CCF}{the cancer cell fraction (CCF) of specified clones}
#' }
#'
'CCF_example_poly'