Coefficients path plot
Coefficients evolution path plot from an object of the class 'LASSO' or 'SSI'
plotPath(fm, Z = NULL, K = NULL, indexK = NULL, tst = NULL, title = NULL, maxCor = 0.85)
fm |
An object of the 'LASSO' or 'SSI' class |
Z |
(numeric matrix) Design matrix for random effects. When |
K |
(numeric matrix) Kinship relationships. This can be a name of a binary file where the matrix is stored. Only needed for a |
indexK |
(integer vector) Which columns and rows will be read when |
tst |
(integer vector) Which individuals are in testing set and to plot. It must be contained in |
title |
(character/expression) Title of the plot |
maxCor |
(numeric) Maximum correlation allowed for two different coefficients. A group of coeffcients with a correlation greater than |
Returns the plot of the coefficients' evolution path along the regularization parameter
Marco Lopez-Cruz (maraloc@gmail.com) and Gustavo de los Campos
require(SFSI) data(wheatHTP) X = scale(X[1:300,])/sqrt(ncol(X)) # Subset and scale markers G = tcrossprod(X) # Genomic relationship matrix y = as.vector(scale(Y[1:300,"YLD"])) # Subset response variable WL = scale(WL[1:300,]) # Reflectance data # Sparse phenotypic regression fm1 = lars2(var(WL),cov(y,WL)) # Sparse family index fm2 = SSI(y,K=G,tst=1:15,trn=16:length(y)) plotPath(fm1) plotPath(fm2,maxCor=0.6) plotPath(fm2,K=G,maxCor=0.6) # Path plot for the first individual in testing set for the SSI plotPath(fm2,K=G,tst=fm2$tst[1])
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