update new function for dwtus

NAMESPACE

@@ -17,6 +17,7 @@ export(getcsv)
 export(getdata)
 export(getdata2)
 export(getdoe)
+export(getdwtus)
 export(getfeaturesanova)
 export(getfeaturest)
 export(getfilter)
@@ -45,6 +46,7 @@ export(getupload3)
 export(gifmr)
 export(ma)
 export(plotden)
+export(plotdwtus)
 export(plote)
 export(plotgroup)
 export(plothist)

R/getmzrt.R

@@ -629,3 +629,17 @@ getoverlaprt <- function(rtrange1, rtrange2) {
         index <- (!is.na(overlapms))
         return(index)
 }
+#' Density weighted intensity for one sample
+#' @param peak peaks intensity one sample
+#' @param n the number of equally spaced points at which the density is to be estimated, default 512
+#' @param log log transformation
+#' @return Density weighted intensity for one sample
+#' @export
+#'
+getdwtus <- function(peak,n=512,log=F){
+        if(log){
+                peak <- log(peak+1)
+        }
+        sum <- sum(density(peak,bw='sj',n=n)$x*density(peak,bw='sj',n=n)$y)
+        return(sum)
+}

R/plotmzrt.R

@@ -760,3 +760,22 @@ plotridges <- function(data, lv, type = "g") {
                                                            bins = 100) + ggplot2::xlim(-0.5, 0.5) + ggplot2::scale_fill_discrete(name = "Group") +
                 ggplot2::labs(x = "Relative Log Abundance", y = "Samples")
 }
+#' plot density weighted intensity for multiple samples
+#' @param list list with data as peaks list, mz, rt and group information
+#' @param n the number of equally spaced points at which the density is to be estimated, default 512
+#' @param ... parameters for `plot` function
+#' @return Density weighted intensity for multiple samples
+#' @examples
+#' data(list)
+#' plotdwtus(list)
+#' @export
+plotdwtus <- function(list,n=512,...){
+        dwtus <- apply(list$data, 2, function(x) getdwtus(x,n = n))
+        if(!is.null(list$order)){
+                plot(dwtus~as.numeric(list$order), xlab='Run order', ylab = 'DWTUS', col = as.numeric(as.factor(list$group)),...)
+                legend('topright',legend = unique(list$group),col = unique(as.numeric(as.factor(list$group))),pch = 19,bty = 'n')
+        }else{
+                plot(dwtus~as.numeric(as.factor(list$group)),xlab='Group', ylab = 'DWTUS',col = as.numeric(as.factor(list$group)),...)
+                legend('topright',legend = unique(list$group),col = unique(as.numeric(as.factor(list$group))),pch = 19,bty = 'n')
+        }
+}