R/heatmap2-plot.R

In ShouyeLiu/metaboliteUtility:

#'  heatmap.2 plot
#'
#' @param data a matrix, see examples
#'
#' @examples
#' data(heatmap_data)
#' metaname <- names(heatmap_data)[4:length(heatmap_data)]
#' subTime <- singleTime <- c("week4","week8")

#' tmp_dataset<- data <- metabolite_data_subset
#' baseline_data <-data[which(data$time %in% c("baseline")),];
#' dataLen <- length(baseline_data);
#' propData = data.frame(BL = rep(0,dataLen-3));
#' for (singleTime in subTime)
#' {
#'     inditmp_dataset <- tmp_dataset[which(tmp_dataset$time %in% singleTime),];
#'     for ( i in 4:dataLen)
#'     {
#'         inditmp_dataset[,i] <-  inditmp_dataset[,i] - baseline_data[,i];
#'     }
#'     is.na(inditmp_dataset[4:dataLen]) <- sapply(inditmp_dataset[4:dataLen],is.infinite);
#'     tmp_dataset2 <- as.data.frame(colMeans(inditmp_dataset[4:dataLen], na.rm = T));
#'     names(tmp_dataset2) <- singleTime;
#'     propData <- cbind(propData,tmp_dataset2 );
#' }
#' tmpMat <- as.matrix(propData[c('BL',subTime)]);
#' tmpHeatmap2 <- genericheatmap2(tmpMat);
#'
#' @details  Please see \link[gplots]{heatmap.2}
#'
#'
#' @name genericheatmap2
#' @rdname genericheatmap2
#' @export
#'



genericheatmap2 <- function(data,
                            main = "cluster analysis",
                            breaks = seq(-1,1, length.out=257),
                            col=gplots::colorpanel(256, 'blue', 'beige', 'red'),
                            dendrogram="row",
                            scale="none",
                            Rowv=T,
                            Colv=T,
                            labRow=rownames(data),
                            sepcolor="black",
                            colsep=c(1,2,3),
                            sepwidth=c(0.025,0.025),
                            rowsep=c(1:nrow(data)),
                            key=T,
                            keysize=1,
                            symkey=TRUE,
                            density.info="none",
                            trace="none",
                            cexRow=0.5,
                            cexCol=0.8,
                            margin=c(5,8),
                            font.axis=1,
                            lmat = matrix(c(4,2,3,1),
                                          nrow=2,
                                          ncol=2),
                            lhei = c(0.08,0.7),
                            lwid = c(0.3,0.7),...
)
{
    tmpHeat <- 	gplots::heatmap.2(data,
                                       breaks = breaks,
                                       col = col,
                                       dendrogram = dendrogram,
                                       scale = scale,
                                       Rowv = Rowv,
                                       Colv = Colv,
                                       labRow = labRow,
                                       sepcolor = sepcolor,
                                       colsep = colsep,
                                       sepwidth = sepwidth,
                                       rowsep = rowsep,
                                       key = key,
                                       keysize = keysize,
                                       symkey = symkey,
                                       density.info = density.info,
                                       trace = trace,
                                       main = main,
                                       cexRow = cexRow,
                                       cexCol = cexCol,
                                       margin = margin,
                                       font.axis = font.axis
                                  ,...
        );
    return (tmpHeat)
}