plot.BioSSA2d: Plot method for class 'BioSSA2d'

In BioSSA/BioSSA: A collection of methods for singular spectrum analysis of drosophila embryo (2d and 3d) gene expression

Description

Plot the decomposition of 2d embryo. Plot graphs from the ‘Rssa’ package for ‘ssa’ object. Also, it can draw two plots of residuals: plot of the corresponding ‘noise.model’ and scatterplot of residuals for different trends reconstructed by different sets of elementary components.

Usage

## S3 method for class 'BioSSA2d'
plot(x, type = c("ssa-values", "ssa-vectors", "ssa-series", "ssa-wcor",
                                      "residuals"), ...)

Arguments

x	object of class ‘BioSSA2d’
type	plot type
...	additional arguments passed to plot functions

Details

For the type parameter 'ssa-*' are just corresponding ‘Rssa’ plots.

For type = 'residuals' one can use following additional arguments:

groups

numeric vector, elementary component indices for trend extraction

groups.y

like previous, used for ‘residuals-vs-residuals’ plot

lm

logical, whether plot linear regression line (with zero offset) on ‘residuals-vs-residuals’ plot

If groups.y is missing then noise model will be estimated and plotted (additional arguments will be passed to both noise.model and plot methods). Otherwise, ‘residuals-vs-residuals’ plot will be plotted.

Value

A Trellis object.

Examples

xlim <- c(22, 88)
ylim <- c(32, 68)
L <- c(15, 15)

file <- system.file("extdata/data", "ab16.txt", package = "BioSSA")
df <- read.emb.data(file)

bss <- BioSSA(cad ~ AP + DV, data = df, ylim = ylim, xlim = xlim, L = L)
plot(bss, type = "ssa-values")
plot(bss, type = "ssa-vectors")
plot(bss, type = "ssa-series", groups = 1:3)

plot(bss, type = "residuals", groups = 1:3)
plot(bss, type = "residuals", groups = 1:3, groups.y = 1:2)

BioSSA/BioSSA documentation built on May 5, 2019, 3:47 p.m.