Merge pull request #54 from SiggiSmara/master

Weighted moving average
sgibb · Nov 12, 2017 · ce2ae33 · ce2ae33
2 parents cce5c67 + 063c32e
commit ce2ae33
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Showing 5 changed files with 52 additions and 7 deletions.
diff --git a/NEWS b/NEWS
@@ -1,5 +1,11 @@
 RELEASE HISTORY OF THE "MALDIquant" PACKAGE
 ===========================================
+CHANGES IN MALDIquant VERSION 1.17:
+--------------------------------------------------
+IMPROVEMENTS
+
+* Added weighted moving average as an option in moving average smoothing of spectra
+
 
 CHANGES IN MALDIquant VERSION 1.16.4 [2017-08-27]:
 --------------------------------------------------

diff --git a/R/smoothingFilters-functions.R b/R/smoothingFilters-functions.R
@@ -1,21 +1,26 @@
-
 ## .movingAverage
 ## runs a simple 2-side moving average.
 ##
 ## params:
 ## y: double, intensity values
-## halfWindowSize integer, half window size.
-##
+## halfWindowSize integer, half window size
+## weighted boolean, if TRUE then applies weighted average, otherwise unweighted average.
 ## returns:
 ## double
 ##
-.movingAverage <- function(y, halfWindowSize=2L) {
+.movingAverage <- function(y, halfWindowSize=2L, weighted=FALSE) {
  .stopIfNotIsValidHalfWindowSize(halfWindowSize, n=length(y))
  windowSize <- 2L * halfWindowSize + 1L
+ if (weighted) {
+ weights <- 1 / 2^abs(-halfWindowSize:halfWindowSize)
+ } else {
+ weights <- rep.int(1L, windowSize)
+ }
  .filter(y, hws=halfWindowSize,
- coef=matrix(1L / windowSize, nrow=windowSize, ncol=windowSize))
+ coef=matrix(weights / sum(weights), nrow=windowSize, ncol=windowSize, byrow=TRUE))
 }
 
+
 ## .savitzkyGolay
 ## runs a savitzky golay filter
 ##

diff --git a/man/smoothIntensity-methods.Rd b/man/smoothIntensity-methods.Rd
@@ -10,7 +10,8 @@ This method smoothes the intensity values of a
 }
 \usage{
 \S4method{smoothIntensity}{MassSpectrum}(object,
- method=c("SavitzkyGolay", "MovingAverage"), halfWindowSize,
+ method=c("SavitzkyGolay", "MovingAverage"),
+ halfWindowSize,
  \dots)
 }
 \arguments{
@@ -26,7 +27,12 @@ This method smoothes the intensity values of a
  selected \code{method}.}
  \item{\dots}{arguments to be passed to \code{method}. \code{SavitzkyGolay} has
  an additional \code{polynomialOrder} argument (default: \code{3}) to control
- the order of the filter. Unused for \code{MovingAverage}}
+ the order of the filter. 
+ \code{MovingAverage} has an additional \code{weighted} argument (default: 
+ \code{FALSE}) to indicate if the average should be equal weight (default) or
+ if it should have weights depending on the distance from the center as 
+ calculated as \code{1/2^abs(-halfWindowSize:halfWindowSize)} with the sum 
+ of all weigths normalized to 1.}
 }
 \details{
  \code{halfWindowSize}: Depends on the selected \code{method}.
@@ -38,6 +44,7 @@ This method smoothes the intensity values of a
 }
 \author{
 Sebastian Gibb \email{mail@sebastiangibb.de}
+Sigurdur Smarason (WeightedAverage smoothing)
 }
 \references{
 A. Savitzky and M. J. Golay. 1964.
@@ -64,6 +71,9 @@ data("fiedler2009subset", package="MALDIquant")
 s <- smoothIntensity(fiedler2009subset, method="MovingAverage",
  halfWindowSize=2)
 ## or
+s <- smoothIntensity(fiedler2009subset, method="MovingAverage",
+ halfWindowSize=2, weighted=TRUE)
+## or
 s <- smoothIntensity(fiedler2009subset, method="SavitzkyGolay",
  halfWindowSize=10)
 }

diff --git a/tests/testthat/test_smoothIntensity-methods.R b/tests/testthat/test_smoothIntensity-methods.R
@@ -20,6 +20,18 @@ test_that("smoothIntensity", {
  expect_equal(intensity(smoothIntensity(s, method="MovingAverage",
  halfWindowSize=2)),
  MALDIquant:::.movingAverage(i, halfWindowSize=2))
+ expect_equal(length(smoothIntensity(s, method="MovingAverage",
+ halfWindowSize=2, weighted=TRUE)), 40)
+ expect_equal(intensity(smoothIntensity(s, method="MovingAverage",
+ halfWindowSize=2, weighted=TRUE)),
+ MALDIquant:::.movingAverage(i, halfWindowSize=2, weighted=TRUE))
+ expect_equal(intensity(smoothIntensity(s, method="MovingAverage",
+ halfWindowSize=2, weighted=TRUE)),
+ intensity(smoothIntensity(s, method="MovingAverage", 
+ weighted=TRUE)))
+ expect_equal(intensity(smoothIntensity(s, method="MovingAverage", 
+ halfWindowSize=2)),
+ intensity(smoothIntensity(s, method="MovingAverage")))
 })
 
 test_that("smoothIntensity works with list of MassSpectrum objects", {

diff --git a/tests/testthat/test_smoothingFilters-functions.R b/tests/testthat/test_smoothingFilters-functions.R
@@ -3,11 +3,23 @@ context("smoothingFilters")
 test_that(".movingAverage", {
  values <- c(rep(3, 3), 4:7, rep(8, 3))
  expect_equal(MALDIquant:::.movingAverage(1:10, halfWindowSize=2), values)
+ expect_equal(MALDIquant:::.movingAverage(1:10, halfWindowSize=2, 
+ weighted=TRUE), values)
 
  values <- c(rep(4, 4), 5:6, rep(7, 4))
  expect_equal(MALDIquant:::.movingAverage(1:10, 3), values)
+ expect_equal(MALDIquant:::.movingAverage(1:10, 3, weighted=TRUE), values)
+
+ signal <- c(rep(1, 4), 6, 20, 6, rep(1, 4))
+ resAve <- c(2.0, 2.0, 2.0, 5.8, 6.8, 6.8, 6.8, 5.8, 2.0, 2.0, 2.0)
+ reswAve <- c(1.5, 1.5, 1.5, 3.9, 7.3,10.6, 7.3, 3.9, 1.5, 1.5, 1.5)
+ expect_equal(MALDIquant:::.movingAverage(signal, halfWindowSize=2, 
+ weighted=FALSE),resAve)
+ expect_equal(MALDIquant:::.movingAverage(signal, halfWindowSize=2, 
+ weighted=TRUE),reswAve)
 })
 
+
 test_that(".movingAverage throws errors", {
  expect_error(MALDIquant:::.movingAverage(1:10, halfWindowSize=0),
  "too small")