evoplot

evoplot is an R package that draws clonal evolution plots based on clonal size counts or clone frequencies

It uses ggplot2 to draw polygons for each subclone and returns a ggplot2 object.

evoplot has been used to plot clonal hierarchies derived from the analysis of hematopoietic progenitor colonies for the publication Somatic Mutations of Calreticulin in Myeloproliferative Neoplasms, Kampfl et al., NEJM 2013

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News

• Version 0.1 released

Installing evoplot

Install the development version directly from github (requires devtools)

require(devtools)
devtools::install_github("sp00nman/evoplot") 

To install a local copy:

evoplot_package <- "~/R/evoplot";
install.packages(evoplot_packages, repos=NULL)

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Usage

library(evoplot)
?evoplot

Evoplot requires input data with the following format:

clone	subclone	colony_count	gene
1	A	25	GENE.A,GENE.B,GENE.C
1	B	15	GENE.A,GENE.B,GENE.C,GENE.D
2	C	10	GENE.E

# basic example
# create dataframe with colony counts for each subclone
df <- data.frame(clone=c(1,1,2),
                 subclone=c("A","B","C"),
                 colony_count=c(25,15,10),
                 gene=c("GENE.A,GENE.B,GENE.C",
                     "GENE.A,GENE.B,GENE.C,GENE.D",
                     "GENE.E")) 

# if necessary, calculate frequencies
df$subcone_freq <- calculate.frequencies(df)

# calculate coordinates to plot polygons
d_plot <- get_coordinates(df, yaxis_length=4, debug=TRUE)

#draw plot
g_plot <- draw.clonal.evolution.plot(d_plot)
print(g_plot)

# save plot to pdf
pdf(paste(path2file, "evoplot.pdf", sep ="/"), 
    width=5, height=5, useDingbats=FALSE)
print(g_plot)
dev.off()