isoPLSDAplot: Plot components from isoPLSDA analysis (pairs plot)

In isomiRs: Analyze isomiRs and miRNAs from small RNA-seq

Description

Plot the most significant components that come from isoPLSDA() analysis together with the density of the samples scores along those components.

Usage

isoPLSDAplot(pls, n = 2)

Arguments

pls	Output from isoPLSDA() function.
n	Number of components to plot.

Details

The function isoPLSDAplot helps to visualize the results from isoPLSDA(). It will plot the samples using the significant components (t1, t2, t3 ...) from the PLS-DA analysis and the samples score distribution along the components. It uses GGally::ggpairs() for the plot.

Value

GGally::ggpairs() plot showing the scores for each sample using isomiRs/miRNAs expression to explain variation.

base::data.frame object with a first column refering to the sample group, and the following columns refering to the score that each sample has for each component from the PLS-DA analysis.

Examples

data(mirData)
# Only miRNAs with > 10 reads in all samples.
ids <- isoCounts(mirData, minc=10, mins=6)
ids <- isoNorm(ids, formula=~condition)
pls.ids <- isoPLSDA(ids, "condition", nperm = 2)
isoPLSDAplot(pls.ids)

isomiRs documentation built on Jan. 31, 2021, 2 a.m.