CoGAPS (version 2.6.0)

plotSmoothPatterns: Plot loess smoothed CoGAPS patterns

Description

Plots the sampled mean value of the pattern matrix ${\bf{P}}$ obtained from the CoGAPS matrix factorization vs. a specificed X value for each sample in the columns of ${\bf{P}}$. Lines plot loess normalized values of ${\bf{P}}$ vs specified X variables.

Usage

plotSmoothPatterns(P, x=NULL, breaks=NULL, breakStyle=T, orderP=!all(is.null(x)), plotPTS=F, pointCol='black', lineCol='grey', add=F, ...)

Arguments

P

A [p, M] pattern matrix (P.mean) obtained from the CoGAPS matrix factorization.

x

A [M, 1] matrix of values for the X axis for each of the corresponding M columns of P. (Optional: Default: x=1:M)

breaks

A vector of X values at which breaks in plotting should occur. Loess lines fit to data will start and stop at breaks. (Optional: Default: no breaks). May also be specified as an integer to determine the number of equal groups into which to divide the data.

breakStyle

A logical vector. If TRUE, the corresponding break will start a new plot on the row for each pattern. If FALSE, a vertical line will demarcate the break point. (Optional: Defaults to all hard breaks). Note, if one logical value is used, that value will determine the break type at each break point.

orderP

A logical value. If TRUE, vertical ordering of patterns will be determined in order of the value of x at which they peak. If FALSE, vertical ordering will be determined by the rows in the P matrix. (Optional: Default: FALSE)

plotPTS

A logical value. If TRUE, plot will include points for each value of the P matrix in addition to the loess smoothed curve. If FALSE, only the loess smoothed values of P will be plotted. (Optional: Default: FALSE)

pointCol

Color of points of the P matrix plotted when plotPTS=TRUE. (Optional: Default: black)

lineCol

Color of loess smoothed values of the P matrix. (Optional: Default: grey)

add

A logical value. If TRUE, plot will be added to existing graphics device. If FALSE, will create a new graphics device. (Optional: Default: FALSE)

...

Additional arguments to plotting functions.

See Also

CoGAPS

Examples

## Not run: 
# # create simulated data
# P <- rbind(1:10 + rnorm(10), seq(from=10,to=1) + rnorm(10))
# 
# # saved as PDF since figure margins are often too large for the null device with this function
# # and the null device may also have trouble with the overlay
# pdf('Test.pdf', width=10)
# plotSmoothPatterns(P=P, x=rep(seq(from=1,to=10,by=2),each=2), breaks=3, breakStyle=c(F,T,T), plotPTS=T)
# 
# # demonstrating the overlay of the plot
# plotSmoothPatterns(P=P, x=rep(seq(from=1,to=10,by=2),each=2), breaks=c(0.992,3.660,6.340,9.010),   breakStyle=c(F,T,T), plotPTS=F, add=T, lineCol='red')
# dev.off()
# ## End(Not run)