plotCordist: Plot distances/correlation between miRNA or mRNA samples

In mariavica/mircomb: An R package for analyzing miRNA-mRNA interactions

Description

Plot distances/correlation between miRNA or mRNA samples

Usage

plotCordist(obj, subset, type = "cor", method.cor = "pearson",
 method.dist = "euclidean", hierarchical = FALSE, ...)

Arguments

obj	a corObject.
subset	"miRNA" or "mRNA"
type	"cor" (correlation) or "dist" (distance).
method.cor	method used for computing correlation: "pearson" or "spearman".
method.dist	method used for computing distance from dist function: This must be one of ‘"euclidean"’, ‘"maximum"’, ‘"manhattan"’, ‘"canberra"’, ‘"binary"’ or ‘"minkowski"’. Any unambiguous substring can be given.
hierarchical	TRUE or FALSE. Sort the rows using hierarchical clustering.
...	further arguments.

Value

A plot of the matrix of distances (or correlations) between samples. A hierarchical clustering of the samples can also be performed to sort the rows and columns.

References

http://www.phaget4.org/R/image_matrix.html

See Also

plot3d, plotPca, dist

Examples

data(data.obj)
plotCordist(data.obj, "miRNA", type="cor")
plotCordist(data.obj, "mRNA", type="dist")

mariavica/mircomb documentation built on Feb. 3, 2020, 2:28 a.m.