plot_emdnull: Plot null distribution of permuted EMD scores vs. calculated...

In EMDomics: Earth Mover's Distance for Differential Analysis of Genomics Data

Description

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

Usage

plot_emdnull(emdobj)

Arguments

emdobj

An EMDomics object, typically returned via a call to calculate_emd.

Value

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

See Also

calculate_emd ggplot

Examples

# 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_emd(dat, groups, nperm=10, parallel=FALSE)
plot_emdnull(results)

Example output

sh: 1: wc: Permission denied
Calculating pairwise emd scores...done.
Calculating emd...done.
Calculating permuted emd #1 of 10...done.
Calculating permuted emd #2 of 10...done.
Calculating permuted emd #3 of 10...done.
Calculating permuted emd #4 of 10...done.
Calculating permuted emd #5 of 10...done.
Calculating permuted emd #6 of 10...done.
Calculating permuted emd #7 of 10...done.
Calculating permuted emd #8 of 10...done.
Calculating permuted emd #9 of 10...done.
Calculating permuted emd #10 of 10...done.
Calculating q-values...done.

EMDomics documentation built on Nov. 8, 2020, 5:30 p.m.