update import based on RGLab/flowStats#16

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/openCyto@109942 bc3139a8-67e5-0310-9ffc-ced21a209358
RGLab · Oct 26, 2015 · e8263ce · e8263ce
1 parent da3132f
commit e8263ce
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Showing 3 changed files with 6 additions and 6 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -12,7 +12,7 @@ LazyLoad: yes
 Depends:
     flowWorkspace(>= 3.11.10)
 Imports:
-    methods,Biobase,gtools,flowCore(>= 1.31.17),flowViz,ncdfFlow(>= 2.11.34),flowStats(>= 3.23.7),flowClust,MASS,clue,plyr,RBGL,graph,data.table,ks,RColorBrewer,lattice,rrcov,R.utils
+    methods,Biobase,gtools,flowCore(>= 1.31.17),flowViz,ncdfFlow(>= 2.11.34),flowStats(>= 3.29.1),flowClust,MASS,clue,plyr,RBGL,graph,data.table,ks,RColorBrewer,lattice,rrcov,R.utils
 Suggests:
     flowWorkspaceData,
     knitr,

diff --git a/NAMESPACE b/NAMESPACE
@@ -94,7 +94,6 @@ importFrom(graph,nodeData)
 importFrom(graph,nodeDataDefaults)
 importFrom(graph,subGraph)
 importFrom(gtools,permutations)
-importFrom(ks,drvkde)
 importFrom(ks,hpi)
 importFrom(methods,coerce)
 importFrom(methods,show)

diff --git a/R/gating-functions.R b/R/gating-functions.R
@@ -955,7 +955,7 @@ cytokine <- function(fr, channel, filterId = "", num_peaks = 1,
 #' Constructs the derivative specified of the kernel density estimate of a
 #' numeric vector
 #'
-#' The derivative is computed with \code{\link[ks:drvkde]{drvkde}}.
+#' The derivative is computed with \code{\link[feature:drvkde]{drvkde}} (feature package 1.2.13)
 #'
 #' For guidance on selecting the bandwidth, see this CrossValidated post:
 #' \url{http://bit.ly/12LkJWz}
@@ -969,17 +969,18 @@ cytokine <- function(fr, channel, filterId = "", num_peaks = 1,
 #' @param adjust a numeric weight on the automatic bandwidth, analogous to the
 #' \code{adjust} parameter in \code{\link{density}}
 #' @param num_points the length of the derivative of the kernel density estimate
-#' @param ... additional arguments passed to \code{\link[ks:drvkde]{drvkde}}
+#' @param ... additional arguments passed to \code{drvkde}
 #' @return list containing the derivative of the kernel density estimate
-#' @importFrom ks hpi drvkde
+#' @importFrom ks hpi 
 .deriv_density <- function(x, deriv = 1, bandwidth = NULL, adjust = 1,
     num_points = 10000, ...) {
 
 
   if (is.null(bandwidth)) {
     bandwidth <- hpi(x, deriv.order = deriv)
   }
-  deriv_x <- drvkde(x = x, drv = deriv, bandwidth = adjust * bandwidth,
+  #we use the private version of drvkde in flowStats (copied from feature package) to avoid the tcltk dependency
+  deriv_x <- flowStats:::drvkde(x = x, drv = deriv, bandwidth = adjust * bandwidth,
       gridsize = num_points, ...)
   list(x = deriv_x$x.grid[[1]], y = deriv_x$est)
 }