R/plotsngls.R

In superOmics/sparsenetgls: Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression

#'The plotsngls() function
#'@description The plotsngls function is designed to provide the line plots
#'of variance of regression coefficients vs. values of penalized parameter 
#'lambda in gls regression, when the tuning parameter d is the maximal value. It
#'also provides the graph structure of the estimated precision matrix in the 
#'penalized path.
#'
#'@import huge 
#'
#'@param fitgls It is a returning object of the sparsnetgls() multivariate
#'generalized least squared regression function.
#'
#'@param lineplot It is a logical indicator. When value=TRUE, it will provide
#'line plot. 
#'
#'@param ncol It is a graph parameter representing number of columns in 
#'the lineplot. 
#'
#'@param nrow It is a graph parameter representing number of rows in 
#'the lineplot. 
#'
#'@param structplot It is a logical indicator. When value=TRUE, it will 
#'provide the structure plot of the specified precision matrix from 
#'the series of the sparsenetgls results. 
#'
#'@param ith_lambda It is the number for the specified precision matrix
#'to be used in the structplot. It represents the ordering number in the
#'precision matrix series from sparsenetgls.    
#'
#'@return Return a plot subject for sparsenetgls including the plot of
#'variance vs lambda and graph structure of the precision matrix estimates. 
#'
#'@examples
#'ndox=5;p=3;n=200
#'VARknown <- rWishart(1, df=4, Sigma=matrix(c(1,0,0,0,1,0,0,0,1),
#'nrow=3,ncol=3))
#'normc <- mvrnorm(n=n,mu=rep(0,p),Sigma=VARknown[,,1])
#'Y0=normc
#'##u-beta
#'u <- rep(1,ndox)
#'X <- mvrnorm(n=n,mu=rep(0,ndox),Sigma=Diagonal(ndox,rep(1,ndox)))        
#'X00 <- scale(X,center=TRUE,scale=TRUE)
#'X0 <- cbind(rep(1,n),X00)
#'#Add predictors of simulated CNA
#'abundance1 <- scale(Y0,center=TRUE,scale=TRUE)+as.vector(X00%*%as.matrix(u))
#'
#'##sparsenetgls()
#'fitgls <- sparsenetgls(responsedata=abundance1,predictdata=X00,
#'nlambda=5,ndist=4,method='lasso')
#'plotsngls(fitgls, ith_lambda=5)
#'#plotsngls(fitgls,lineplot=TRUE,structplot=FALSE,nrow=2,ncol=3)
#'@export

plotsngls<- function(fitgls,lineplot = FALSE,nrow,ncol,structplot = TRUE,
                ith_lambda = 1) {
lambda <- fitgls$lambda;    nlambda <- length(lambda)
covBeta <- fitgls$covBet;    ndist <- fitgls$power-1
# line-plot
if (lineplot == TRUE) {
par(mfrow = c(nrow, ncol))
beta <- fitgls$beta
ndox <- length(beta[, 1])
nq = nrow * ncol
    
        if (ndist>1)
{for (i in seq_len(nq)) {
        maxcov <- max(covBeta[i, i, ndist, ], na.rm = TRUE)
        mincov <- min(covBeta[i, i, ndist, ], na.rm = TRUE)
        grid = (maxcov - mincov)/10
        plot(lambda, covBeta[i, i, ndist, ], main = paste("beta", 
                                                        i - 1, sep = ""),
        xlab = "lambda",
        ylab = "Estimated variance of beta", 
        type = "p", pch = 19, ylim = c(mincov -
                                            mincov/10, maxcov + maxcov/10))
        lines(lambda, covBeta[i, i, ndist, ])
        if (i == nq) 
        legend(lambda[nlambda], round(maxcov, 4) - grid, bty = "n",
        lty = 1, paste("max tuning d=", ndist))}
        }  
        else if (ndist==1)
        {
        for (i in seq_len(nq)) {
        maxcov <- max(covBeta[i, i, ], na.rm = TRUE)
        mincov <- min(covBeta[i, i, ], na.rm = TRUE)
        grid = (maxcov - mincov)/10
        plot(lambda, covBeta[i, i, ], main = paste("beta", i - 1, sep = ""), 
        xlab = "lambda", 
        ylab = "Estimated variance of beta", 
        type = "p", pch = 19, ylim = c(mincov, maxcov))
        lines(lambda, covBeta[i, i, ])
        if (i == nq) 
        legend(lambda[nlambda], round(maxcov, 4) - grid, bty = "n",
                lty = 1, paste("max tuning d=", ndist))}
        }    
                }
# graph-structure
if (structplot == TRUE) {
        PREC_seq <- fitgls$PREC_seq
        precdim = dim(fitgls$PREC_seq[[1]])[1]
        adj <- convert_to_adj(fitgls$PREC_seq[[ith_lambda]],p = precdim)
        huge.plot(adj, graph.name = "precision matrix")}
}