plot_cvm_density: Plot distributions and CVM score for a gene.
In EMDomics: Earth Mover's Distance for Differential Analysis of Genomics Data

Description Usage Arguments Value See Also Examples

The data for the specified gene is retrieved from cvmobj$data. outcomes is used to divide the data into distributions for each group, which are then visualized as density distributions. The calculated CVM score for the specified gene is displayed in the plot title.

1	plot_cvm_density(cvmobj, gene_name)

`cvmobj`	An `CVMomics` object, typically returned via a call to `calculate_cvm`.
`gene_name`	The gene to visualize. The name should be defined as a row name in `cvmobj$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="")

# "A": first 50 samples; "B": next 30 samples; "C": final 20 samples
outcomes <- c(rep("A",50), rep("B",30), rep("C",20))
names(outcomes) <- colnames(dat)

results <- calculate_cvm(dat, outcomes, nperm=10, parallel=FALSE)
plot_cvm_density(results, "gene5")