R/CompromisePlot.R

In Yuliaxis/LinkHD: LinkHD: a versatile framework to explore and integrate heterogeneous data

#' @title Compromise-Plot
#' @description Plot a \code{CompromisePlot} of a DiStatis object
#'
#'
#' @param x DistStatis class object.
#' @param x_lab a character indicating x_label. Default is x.
#' @param y_lab a character indicating y_label. Default is y.
#' @param Name a character indicating plot title.
#' @param pchPoints pch for points in scatter plot.
#' @param colObs is a  character indicating the color for the observations. By Default is the QR (indicating the Quality of Representation of observations)
#' @param ... additional parameters from ggplot2 library
#'
#' @return plotted CompromisePlot/s of the component/s of the given DistStatis object.
#'
#' @author Laura M. Zingaretti
#'
#' @examples
#' {
#'
#'data(Taraoceans)
#'pro.phylo <- Taraoceans$taxonomy[ ,'Phylum']
#'TaraOc<-list(Taraoceans$phychem,as.data.frame(Taraoceans$pro.phylo),
#'as.data.frame(Taraoceans$pro.NOGs))
#'TaraOc_1<-scale(TaraOc[[1]])
#'Normalization<-lapply(list(TaraOc[[2]],TaraOc[[3]]),
#'function(x){DataProcessing(x,Method='Compositional')})
#'colnames(Normalization[[1]])=pro.phylo
#'colnames(Normalization[[2]])=Taraoceans$GO
#'TaraOc<-list(TaraOc_1,Normalization[[1]],Normalization[[2]])
#'names(TaraOc)<-c('phychem','pro_phylo','pro_NOGs')
#'TaraOc<-lapply(TaraOc,as.data.frame)
#'Output<-LinkData(TaraOc,Scale =FALSE,Distance = c('ScalarProduct','Euclidean','Euclidean'))
#'CompromisePlot(Output) +
#'theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
#'panel.background = element_blank(), axis.line = element_line(colour = 'black'))
#'
#'
#' }
#' @exportMethod CompromisePlot
#' @docType methods
#' @usage \S4method{CompromisePlot}{DistStatis}(x,x_lab=NULL, y_lab=NULL,
#' Name=NULL, pchPoints=2, colObs=NULL,...)
#' @name CompromisePlot
#' @rdname DistStatis-CompromisePlot
#' @inheritParams DistStatis
#' @aliases CompromisePlot,DistStatis-method
#' @import ggplot2
#' @import graphics
#'



setGeneric("CompromisePlot", def = function(x, x_lab = NULL, y_lab = NULL, Name = NULL, pchPoints = 2, colObs = NULL, 
    ...) {
    standardGeneric("CompromisePlot")
})



setMethod(f = "CompromisePlot", c("DistStatis"), definition = function(x, x_lab = NULL, y_lab = NULL, Name = NULL, 
    pchPoints = 2, colObs = NULL, ...) {
    
    
    PARACCIND <- compromise_coords(x)
    colnames(PARACCIND) <- paste0("Dim", seq_len(ncol(PARACCIND)))
    if (is.null(x_lab)) {
        x_lab = paste0("Dim 1( ", round(Inertia_comp(x)[1, 2], 2), " %)")
    }
    if (is.null(y_lab)) {
        y_lab = paste0("Dim 2( ", round(Inertia_comp(x)[2, 2], 2), " %)")
    }
    
    if (is.null(colObs)) {
        colObs <- RQO(x)$`RQI(%)`
        QR <- colObs
    } else {
        QR <- colObs
    }
    
    ggplot2::ggplot(PARACCIND, aes(x = PARACCIND[, 1], y = PARACCIND[, 2])) + geom_point(size = pchPoints, aes(color = QR)) + 
        labs(x = x_lab, y = y_lab) + ggtitle(Name)
    
    
})