An R package for visualizing changes in the subclonal architecture of tumors

Installation instructions:

#install devtools if you don't have it already for easy installation
install.packages("devtools")
library(devtools)
install_github("chrisamiller/fishplot")

If you prefer to build the package by hand, follow these steps:

• Make sure that you have the dependencies from CRAN ("Hmisc","plotrix","png")

• Download and build from source:

    git clone [email protected]:chrisamiller/fishplot.git
    R CMD build fishplot
    R CMD INSTALL fishplot_0.1.tar.gz
  

Usage

    library(fishplot)

    #provide a list of timepoints to plot
    #You may need to add interpolated points to end up with the desired
    #visualization. Example here was actually sampled at days 0 and 150
    timepoints=c(0,30,75,150)      

    #provide a matrix with the fraction of each population
    #present at each timepoint
    frac.table = matrix(
      c(100, 45, 00, 00,
         02, 00, 00, 00,
         02, 00, 02, 01,
         98, 00, 95, 40),
      ncol=length(timepoints))

    #provide a vector listing each clone's parent
    #(0 indicates no parent)
    parents = c(0,1,1,3)

    #create a fish object
    fish = createFishObject(frac.table,parents,timepoints=timepoints)

    #calculate the layout of the drawing
    fish = layoutClust(fish)

    #draw the plot, using the splining method (recommended)
    #and providing both timepoints to label and a plot title
    drawPlot(fish,shape="spline",title.btm="Sample1",
             cex.title=0.5, vlines=c(0,150), 
             vlab=c("day 0","day 150"))

Outputs

see the vignettes (to be completed soon) for more examples and code

Simple plot with multiple subclones

More complex clonal structure

Multiple independent clones, many timepoints

FAQ

Q: Why "fishplot"? A: The original visualization was put together by Joshua McMichael for a paper on relapsed AML. Upon seeing the plots, someone remarked they looked like a tropical fish, and the name stuck.

Notes

Manuscript in preparation.