plot_cvmnull: Plot null distribution of permuted cvm scores vs. calculated...
In EMDomics: Earth Mover's Distance for Differential Analysis of Genomics Data

Description Usage Arguments Value See Also Examples

The median of the randomly permuted CVM scores (i.e. the null distribution) is plotted on the x-axis, vs. the observed CVM scores on the y-axis. The line y=x is superimposed.

1	plot_cvmnull(cvmobj)

cvmobj

An CVMomics object, typically returned via a call to calculate_cvm.

A ggplot object is returned. If the value is not assigned, a plot will be drawn.

calculate_cvm ggplot

# 100 genes, 100 samples
dat <- matrix(rnorm(10000), nrow=100, ncol=100)
rownames(dat) <- paste("gene", 1:100, sep="")
colnames(dat) <- paste("sample", 1:100, sep="")

# "group A" = first 50, "group B" = second 50
groups <- c(rep("A",50),rep("B",50))
names(groups) <- colnames(dat)

results <- calculate_cvm(dat, groups, nperm=10, parallel=FALSE)
plot_cvmnull(results)