R/plot.R

In daijiang/dli55: Functions collected/wrote by Daijiang Li

# Multiple plot function
#' \code{multiplot} to put ggplot objects in multiple panels
#' 
#' @author Wilston Chang http://www.cookbook-r.com/Graphs/Multiple_graphs_on_one_page_(ggplot2)/
#' 
#' @param ... ggplot objects
#' @param plotlist a list of ggplot objects.
#' @param cols Number of columns in layout.
#' @param layout A matrix specifying the layout. If present, 'cols' is ignored.
#' If the layout is something like matrix(c(1,2,3,3), nrow=2, byrow=TRUE),
#' then plot 1 will go in the upper left, 2 will go in the upper right, and
#' 3 will go all the way across the bottom.
#' @export
multiplot <- function(..., plotlist = NULL, file, cols = 1, layout = NULL) {
    require(grid)
    
    # Make a list from the ... arguments and plotlist
    plots <- c(list(...), plotlist)
    
    numPlots = length(plots)
    
    # If layout is NULL, then use 'cols' to determine layout
    if (is.null(layout)) {
        # Make the panel ncol: Number of columns of plots nrow: Number of rows needed, calculated from # of cols
        layout <- matrix(seq(1, cols * ceiling(numPlots/cols)), ncol = cols, nrow = ceiling(numPlots/cols))
    }
    
    if (numPlots == 1) {
        print(plots[[1]])
        
    } else {
        # Set up the page
        grid.newpage()
        pushViewport(viewport(layout = grid.layout(nrow(layout), ncol(layout))))
        
        # Make each plot, in the correct location
        for (i in 1:numPlots) {
            # Get the i,j matrix positions of the regions that contain this subplot
            matchidx <- as.data.frame(which(layout == i, arr.ind = TRUE))
            
            print(plots[[i]], vp = viewport(layout.pos.row = matchidx$row, layout.pos.col = matchidx$col))
        }
    }
}

# Panel of pairs() function
#' \code{panel.cor} to plot absolute value of correlations
#' 
#' @export
panel.cor <- function(x, y, digits = 2, prefix = "", cex.cor, color.threshold = 0.5, ...) {
    usr <- par("usr")
    on.exit(par(usr))
    par(usr = c(0, 1, 0, 1))
    z = na.omit(data.frame(x = x, y = y))
    r <- cor(z$x, z$y)
    txt <- format(c(r, 0.123456789), digits = digits)[1]
    txt <- paste0(prefix, txt)
    if (missing(cex.cor)) 
        cex.cor <- 0.9/strwidth(txt)
    color.cor = ifelse(abs(r) > color.threshold, "red", "black")
    text(0.5, 0.5, txt, cex = 2, col = color.cor)
    # text(0.5, 0.5, txt, cex = 7*cex.cor * r)
}

# Panel of pairs() function
#' \code{panel.hist} to plot absolute value of correlations
#' 
#' @export
panel.hist <- function(x, ...) {
    usr <- par("usr")
    on.exit(par(usr))
    par(usr = c(usr[1:2], 0, 1.5))
    h <- hist(x, plot = FALSE)
    breaks <- h$breaks
    nB <- length(breaks)
    y <- h$counts
    y <- y/max(y)
    rect(breaks[-nB], 0, breaks[-1], y, col = "lightblue", ...)
}