plot.geneARMA {geneARMA}R Documentation

Plot method for "geneARMA" objects. Displays fitted models and gene expression by group and time.

Description

Produces two types of plots depending on "type" variable. The first, "all.means," shows all periodic signals fitted to each of the clusters, with the last cluster, which is typically used for the group of genes with no abnormal expression, colored black. The second type of plot shows the gene experssion values by time with the fitted mean overlayed.

Usage

 
## S3 method for class 'geneARMA':
plot(x, y=NULL, type = c("all.means", "single.cluster"), j, ...)

Arguments

x A fitted model object of class "geneARMA" produced by geneARMAfit(...).
y Unused. Supplied for compatability with plot method.
type all.means produces a plot of all cluster means. single.cluster plots the data for a single cluster with the mean overlayed.
j is used to indicate which cluster to plot for single.cluster plots only.
...

Author(s)

Timothy McMurry and Arthur Berg

References

Ning Li, et al. Functional clustering of periodic transcriptional profiles through ARMA(p,q)

Examples

set.seed(100)
Data <- geneARMAsim(400, ars=c(.5, .1))
f1 <- geneARMAfit(Data$Y, Data$tm, 2, 2, 2, 0, eps.conv = .001, max.iter = 15, tau.init=c(.25, .45))
plot(f1, y=NULL, "all.means")
plot(f1, y=NULL, "single.cluster", j=2)

[Package geneARMA version 1.0 Index]