An R package for visualizing changes in the subclonal architecture of tumors
This package is still in beta, and there may be minor changes to the parameters over the next few weeks.
#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
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 = layoutClones(fish)
#draw the plot, using the splining method (recommended)
#and providing both timepoints to label and a plot title
fishPlot(fish,shape="spline",title.btm="Sample1",
cex.title=0.5, vlines=c(0,150),
vlab=c("day 0","day 150"))
The tests/ directory contains several examples that explore many of the features in detail. Some example outputs are below.
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.
Manuscript in preparation.