R/eco.forestplot.R

In EcoGenetics: Management and Exploratory Analysis of Spatial Data in Landscape Genetics

#' Forestplot graphs
#' 
#' @description This program generates a forest plot 
#' for the confidence interval of each individual of the
#' input data (as row number)
#' and the corresponding observed value of the statistic.
#' 
#' @param input Matrix/data frame, with three columns in the 
#' folowing order: observed value, lower and upper values of the 
#' confidence interval. 
#' @param xlabel Optional label for x axis.
#' @param ylabel Optional label for y axis.
#' @param titlelabel Optional title label.
#' @param legendlabel Optional legend label.
#' @param rescaled rescale values to [-1, 1] range?
#' @param interactivePlot Show an interactive plot via plotly? (default: TRUE)
#' @param ... Additional elements to the generic.
#' 
#' @examples
#' \dontrun{
#' 
#' require(ggplot2)
#' # simulated confidence intervals for the null hypotesis of a variable "a"
#' set.seed(8)
#' a<-runif(10, -2, 2)
#' infer <- runif(10, -1, 1)
#' super <- runif(10, -1, 1)
#' infer2 <- pmin(infer, super)
#' super2 <- pmax(infer, super)
#' data <- data.frame(a, infer2, super2)
#' forest <- eco.forestplot(data)
#' forest
#' 
#' # the forestplot method support the use of ggplot2 syntax with ggplot2 graphs
#' forest <- eco.forestplot(data, interactivePlot = FALSE)
#' forest <- forest + theme_bw() + theme(legend.position="none")
#' forest
#' }
#' 
#' 
#' @rdname forestplot-methods
#' 
#' @aliases eco.forestplot,generic-method
#' 
#' @author Leandro Roser \email{learoser@@gmail.com}
#' 
#' @exportMethod eco.forestplot

setGeneric("eco.forestplot", 
           function(input, 
                    xlabel = NULL,
                    ylabel = NULL,
                    titlelabel = NULL,
                    legendlabel = NULL,
                    interactivePlot = TRUE,
                    ...) {
             standardGeneric("eco.forestplot")
           })



#' @rdname forestplot-methods
#' @aliases eco.forestplot,eco.lsa-method
#' @exportMethod eco.forestplot

setMethod("eco.forestplot", 
          "eco.lsa",
          function(input,
                   rescaled = FALSE,
                   xlabel,
                   ylabel,
                   titlelabel,
                   legendlabel,
                   interactivePlot = TRUE) {
            
            obs2 <- NULL
            
            if(interactivePlot) {
              axis.size <- 9
              title.size <- 13
              point.size <- 1.2
            } else {
              axis.size <- 10
              title.size <- 14
              point.size <- 0.9
            }
            
            if(input@TEST != "bootstrap") {
              stop("this method is available for eco.lsa with bootstrap test")
            }
            
            datos <- input@OUT
            
            ind <- rownames(datos)
            
            if(rescaled) {
              obs <- datos$obs.res
            } else {
              obs <- datos$obs
            }
            message(paste("plot options: rescaled =", rescaled))
            
            lwr <- datos$lwr
            uppr <- datos$uppr
            method <- input@METHOD
            
            data.select <- data.frame(ind, obs, lwr, uppr)
            
            
            
            if(is.null(xlabel)) {
              xlabel <- method
            } 
            
            if(is.null(ylabel)) {
              ylabel <- "Individual"
            } 
            
            if(is.null(titlelabel)) {
              titlelabel <- " "
            }
            
            if(is.null(legendlabel)) {
              legendlabel <- paste("  ", method)
            }
            
            data.select$obs2 <- obs
            p <- ggplot2::ggplot(data.select, ggplot2::aes(x = c(1:length(ind)), 
                                                           y = obs2, 
                                                           ymin = lwr,
                                                           ymax = uppr)) + 
              ggplot2::geom_pointrange(ggplot2::aes(colour = obs), size=0.9) +
              #ggplot2::geom_point(size=2.5,  shape=1) +
              #ggplot2::geom_point(size=2.7,  shape=1) +
              
              #ggplot2::geom_line(ggplot2::aes(x= XVALUE, y = YVALUE), lwd = 1, alpha = 0.4) + 
              ggplot2::coord_flip() + 
              ggplot2::scale_colour_gradient(legendlabel, 
                                             low = "green", 
                                             high = "red") +
              ggplot2::ylab(xlabel) +
              ggplot2::xlab(ylabel) +
              ggplot2::labs(title = titlelabel)+
              ggplot2::theme(axis.text = ggplot2::element_text(size = axis.size), 
                             axis.title = ggplot2::element_text(size = title.size), 
                             plot.title = ggplot2::element_text(size = title.size, hjust=0.5))
            attr(p, "data") <- data.select
            if(interactivePlot) {
              p <-suppressMessages(plotly::ggplotly(p, tooltip = c("obs", "lwr", "uppr")))
            }
            message(paste("plot options: interactivePlot =", interactivePlot))
            p
            
          })


#' @rdname forestplot-methods
#' @aliases eco.forestplot,dataframeORmatrix-method
#' @exportMethod eco.forestplot

setMethod("eco.forestplot", 
          "dataframeORmatrix",
          function(input,
                   xlabel,
                   ylabel,
                   titlelabel,
                   legendlabel,
                   interactivePlot = TRUE) {
            
            
            obs2 <- NULL
            
            if(interactivePlot) {
              axis.size <- 9
              title.size <- 13
              point.size <- 1.2
            } else {
              axis.size <- 10
              title.size <- 14
              point.size <- 0.9
            }
            
            datos <- input
            
            ind <- rownames(datos)
            obs <- datos[, 1]
            lwr <- datos[, 2]
            uppr <- datos[, 3]
            
            data.select <- data.frame(ind, obs, lwr, uppr)
            
            if(is.null(xlabel)) {
              xlabel <- "value"
            } 
            
            if(is.null(ylabel)) {
              ylabel <- "Individual"
            } 
            
            if(is.null(titlelabel)) {
              titlelabel <- ""
            }
            
            if(is.null(legendlabel)) {
              legendlabel <- ""
            }
            
            data.select$obs2 <- obs
            p <- ggplot2::ggplot(data.select, ggplot2::aes(x = c(1:length(ind)), 
                                                           y = obs2, 
                                                           ymin = lwr,
                                                           ymax = uppr)) + 
              ggplot2::geom_pointrange(ggplot2::aes(colour = obs), size= point.size) +
              ggplot2::scale_colour_gradient(low = "blue", 
                                             high = "red") +
              #ggplot2::geom_point(size=2.5,  shape=1) +
              #ggplot2::geom_point(size=2.7,  shape=1) +
              ggplot2::coord_flip() +  
              ggplot2::ylab(xlabel) +
              ggplot2::xlab(ylabel) +
              ggplot2::labs(title = titlelabel)+
              ggplot2::theme(axis.text = ggplot2::element_text(size = axis.size), 
                             axis.title = ggplot2::element_text(size = title.size), 
                             plot.title = ggplot2::element_text(size = title.size, hjust=0.5))
            
            if(interactivePlot) {
              p <- suppressMessages(plotly::ggplotly(p, tooltip = c("obs", "lwr", "uppr")))
            }
            
            attr(p, "data") <- data.select
            p
            
          })