R/correplot.R

In ShouyeLiu/metaboliteUtility:

#'  Correlation plot for data
#'
#'
#' @param pearsoncorr  person correlation matrix
#'
#' @details  Please see \link[corrplot]{corrplot}
#'
#' @examples
#'  library(Hmisc)
#'  data(corrplot_data)
#'  tmpDataset <- as.matrix(corrplot_data);
#'  tmpPearsonCorr <- Hmisc::rcorr(tmpDataset,type="pearson");
#'  tmpPearsonMat <- tmpPearsonCorr$r;
#'  diag(tmpPearsonMat) <- 0;
#'  tmpPearsonMat[lower.tri(tmpPearsonMat)] <- 0;
#'  tmpCorrplot <- genericcorrplot(tmpPearsonCorr,title="Pearson correlation analysis");
#'
#'
#' @name genericcorrplot
#' @rdname genericcorrplot
#' @export
#'




genericcorrplot <- function(pearsoncorr,
                            title = "Correlation map",
                            method = "circle",
                            type = "upper",
                            add = FALSE,
                            col = grDevices::colorRampPalette(c("blue","white","red"))(200),
                            bg = "white",
                            is.corr = TRUE,
                            diag = FALSE,
                            outline = TRUE,
                            oma = c (0,0,0,0),
                            mar = c(0,0,2,0),
                            addgrid.col = NULL,
                            addCoef.col = NULL,
                            addCoefasPercent = FALSE,
                            order = "original",
                            tl.pos = "td",
                            tl.cex = 0.75,
                            tl.col = "black",
                            tl.offset = 0.4,
                            tl.srt = 55,
                            cl.pos = NULL,
                            cl.lim = NULL,
                            cl.length = NULL,
                            cl.cex = 0.8,
                            cl.ratio = 0.15,
                            cl.align.text = "c",
                            cl.offset = 0.5,
                            number.cex = 0.7,
                            addshade = c("negative", "positive", "all"),
                            shade.lwd = 1,
                            shade.col = "white",
                            p.mat = pearsoncorr$P ,
                            sig.level = 0.05,
                            insig = "blank",
                            pch = 6,
                            pch.col = "black",
                            pch.cex = 2,
                            plotCI = "n",...
)
{
    tmpCorrplot <- corrplot:::corrplot(pearsoncorr$r,
                                           title = title,
                                           method = method,
                                           type = type,
                                           add = add,
                                           col = col,
                                           bg = bg,
                                           is.corr = is.corr,
                                           diag = diag,
                                           outline = outline,
                                           oma = oma,
                                           mar = mar,
                                           addgrid.col = addgrid.col,
                                           addCoef.col = addCoef.col,
                                           addCoefasPercent = addCoefasPercent,
                                           order = order,
                                           tl.pos = tl.pos,
                                           tl.cex = tl.cex,
                                           tl.col = tl.col,
                                           tl.offset = tl.offset,
                                           tl.srt = tl.srt,
                                           cl.pos = cl.pos,
                                           cl.lim = cl.lim,
                                           cl.length = cl.length,
                                           cl.cex = cl.cex,
                                           cl.ratio = cl.ratio,
                                           cl.align.text = cl.align.text,
                                           cl.offset = cl.offset,
                                           number.cex = number.cex,
                                           addshade = addshade,
                                           shade.lwd = shade.lwd,
                                           shade.col = shade.col,
                                           p.mat = p.mat ,
                                           sig.level = sig.level,
                                           insig = insig,
                                           pch = pch,
                                           pch.col = pch.col,
                                           pch.cex = pch.cex,
                                           plotCI = plotCI,...);
    return(tmpCorrplot)
}