More RGLab/flowWorkspace#274

Author: jacobpwagner

NAMESPACE

@@ -1,7 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(as.data.table,gatingTemplate)
-export(.between_interval)
+S3method(gt_gating,gatingTemplate)
 export(add_pop)
 export(add_pop_init)
 export(cytokine)
@@ -10,41 +10,50 @@ export(flowClust.1d)
 export(flowClust.2d)
 export(gate_flowClust_1d)
 export(gate_flowClust_2d)
+export(gate_flowclust_1d)
+export(gate_flowclust_2d)
 export(gate_mindensity)
 export(gate_mindensity2)
 export(gate_quad_sequential)
 export(gate_quad_tmix)
 export(gate_quantile)
 export(gate_tail)
+export(gate_tautstring)
 export(gating)
 export(gatingTemplate)
 export(get.helperGates)
+export(gh_generate_template)
+export(gs_add_pop)
+export(gs_add_pop_init)
+export(gs_remove_pop)
+export(gt_delete_helpergates)
+export(gt_gating)
+export(gt_get_children)
+export(gt_get_gate)
+export(gt_get_helpergates)
+export(gt_get_parent)
+export(gt_get_pop_paths)
+export(gt_toggle_helpergates)
 export(listgtMethods)
 export(mindensity2)
 export(prior_flowClust)
 export(quadGate.seq)
 export(quadGate.tmix)
 export(quantileGate)
-export(registerGatingFunction)
 export(registerPlugins)
+export(register_plugins)
 export(remove_pop)
 export(tautString)
+export(tautStringGate)
+export(tautstring)
 export(templateGen)
 export(toggle.helperGates)
 exportClasses(gatingTemplate)
-exportClasses(gtMethod)
-exportClasses(gtPopulation)
-exportClasses(polyFunctions)
-exportClasses(ppMethod)
 exportMethods(add)
-exportMethods(dims)
-exportMethods(gating)
 exportMethods(getChildren)
 exportMethods(getGate)
 exportMethods(getNodes)
 exportMethods(getParent)
-exportMethods(names)
-exportMethods(parameters)
 exportMethods(plot)
 exportMethods(show)
 import(data.table)

R/AllClasses.R

@@ -26,7 +26,7 @@
 #' @examples
 #' \dontrun{gatingTemplate('test.csv')}
 #' @seealso See \code{\link[openCyto:gating-methods]{gating}}, 
-#' \code{\link{flowClust.1d}}, 
+#' \code{\link{gate_flowclust_1d}}, 
 #' for an overview of gating functions.
 NULL
 
@@ -177,7 +177,6 @@ fcTree <- function(gt) {
 #' 
 #' 
 #' @rdname gtMethod-class 
-#' @export 
 #' @name gtMethod-class
 #' @aliases gtMethod
 #' @examples 
@@ -198,7 +197,6 @@ setClass("gtMethod", representation(name = "character"
 #' 
 #' It extends \code{gtMethod} class.
 #' 
-#' @export      
 #' @name ppMethod-class
 #' @aliases ppMethod
 #' @examples 
@@ -236,7 +234,6 @@ setClass("boolMethod", contains = "refGate")
 #' 
 #' It extends \code{boolMethod} class and will be expanded to multiple \code{boolMethod} object.
 #' 
-#' @export
 #' @name polyFunctions-class
 setClass("polyFunctions", contains = "boolMethod")
 
@@ -249,13 +246,12 @@ setClass("polyFunctions", contains = "boolMethod")
 #'  \item{name}{ \code{character} the name of population}
 #'  \item{alias}{ \code{character} the more user friendly name of population}
 #' }
-#' @export 
 #' @name gtPopulation-class
 #' @examples 
 #'  \dontrun{
 #'      gt <- gatingTemplate(system.file("extdata/gating_template/tcell.csv",package = "openCyto"))
 #'       
-#'      getNodes(gt, '2')
+#'      gt_get_pop_paths(gt, '2')
 #' }
 setClass("gtPopulation", representation(id = "character", name = "character",
                                         alias = "character"
@@ -363,7 +359,7 @@ setGeneric("gatingTemplate", function(x, ...) standardGeneric("gatingTemplate"))
 #' @param x \code{character} csv file name
 #' @param name \code{character} the label of the gating template
 #' @param strict \code{logical} whether to perform validity check(special characters) on the alias column. By default it is(and should be) turned on for the regular template parsing. 
-#'                              But sometime it is useful to turned it off to bypass the check for the dummy nodes(e.g. the csv template generated by 'templateGen'  with some existing boolean gates that has '!' or ':' symbol).
+#'                              But sometime it is useful to turned it off to bypass the check for the dummy nodes(e.g. the csv template generated by 'gh_generate_template'  with some existing boolean gates that has '!' or ':' symbol).
 #' @param strip_extra_quotes \code{logical} Extra quotes are added to strings by fread. This causes problems with parsing R strings to expressions in some cases. Default FALSE for usual behaviour. TRUE should be passed if parsing gating_args fails.
 #' @param ... other arguments passed to \code{data.table::fread}
 #' @importFrom graph graphNEL addEdge edges nodeDataDefaults nodeData edgeDataDefaults addEdge edgeData subGraph

R/add.R

@@ -15,7 +15,6 @@ setClass("ocRectangleGate", contains = "rectangleGate", representation(ind = "ra
 #' @param action \code{ocRectangleGate} or \code{logicalFilterResult}
 #' @param recompute \code{logical} see \link[flowWorkspace]{add} in \code{flowWorkspace} package
 #' @param ... see \link[flowWorkspace]{add} in \code{flowWorkspace} package
-#' @export 
 #' @rdname add
 setMethod("add",
     signature=c("GatingHierarchy", "ocRectangleGate"),