Merge pull request #269 from amcdavid/docupdate

Freshen docs

Author: amcdavid

.Rbuildignore

@@ -8,3 +8,4 @@ Makefile
 ^docs$
 ^pkgdown$
 ^misc$
+^\.github/

DESCRIPTION

@@ -40,4 +40,4 @@ biocViews: ImmunoOncology, FlowCytometry, DataImport, Preprocessing, DataReprese
 Encoding: UTF-8
 VignetteBuilder: knitr
 LinkingTo: cpp11
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2

NAMESPACE

@@ -1,13 +1,16 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(as.data.table,gatingTemplate)
+S3method(gt_gating,dummyMethod)
 S3method(gt_gating,gatingTemplate)
 S3method(pop_add,ocRectRefGate)
 export(CytoExploreR_.argDeparser)
 export(CytoExploreR_.preprocess_csv)
+export(CytoExploreR_.preprocess_row)
 export(add_pop)
 export(add_pop_init)
 export(delete.helperGates)
+export(fast_rlm)
 export(flowClust.1d)
 export(flowClust.2d)
 export(gate_flowClust_1d)
@@ -21,6 +24,7 @@ export(gate_quad_tmix)
 export(gate_quantile)
 export(gating)
 export(gatingTemplate)
+export(generate_gate_template)
 export(get.helperGates)
 export(gh_generate_template)
 export(gs_add_gating_method)
@@ -81,24 +85,43 @@ importClassesFrom(ncdfFlow,ncdfFlowSet)
 importFrom(BiocGenerics,dims)
 importFrom(RBGL,tsort)
 importFrom(RColorBrewer,brewer.pal)
+importFrom(data.table,fwrite)
 importFrom(flowClust,dmvt)
 importFrom(flowClust,dmvtmix)
 importFrom(flowClust,flowClust)
 importFrom(flowClust,getEstimates)
 importFrom(flowClust,rbox)
 importFrom(flowClust,tmixFilter)
 importFrom(flowCore,"%in%")
+importFrom(flowCore,"exprs<-")
 importFrom(flowCore,"filterDetails<-")
 importFrom(flowCore,"parameters<-")
 importFrom(flowCore,colnames)
+importFrom(flowCore,exprs)
+importFrom(flowCore,filters)
 importFrom(flowCore,getChannelMarker)
 importFrom(flowCore,identifier)
 importFrom(flowCore,parameters)
+importFrom(flowCore,polygonGate)
+importFrom(flowCore,quadGate)
+importFrom(flowCore,rectangleGate)
+importFrom(flowWorkspace,cf_lock)
+importFrom(flowWorkspace,cf_unlock)
+importFrom(flowWorkspace,gh_get_pop_paths)
+importFrom(flowWorkspace,gh_get_transformations)
+importFrom(flowWorkspace,gh_pop_get_data)
+importFrom(flowWorkspace,gh_pop_get_gate)
 importFrom(flowWorkspace,gh_pop_is_negated)
 importFrom(flowWorkspace,gh_pop_set_visibility)
 importFrom(flowWorkspace,gs_get_pop_paths)
 importFrom(flowWorkspace,gs_pop_get_children)
 importFrom(flowWorkspace,identifier)
+importFrom(flowWorkspace,pData)
+importFrom(flowWorkspace,realize_view)
+importFrom(flowWorkspace,sampleNames)
+importFrom(flowWorkspace,transform)
+importFrom(flowWorkspace,transformerList)
+importFrom(grDevices,chull)
 importFrom(graph,"edgeData<-")
 importFrom(graph,"edgeDataDefaults<-")
 importFrom(graph,"nodeData<-")
@@ -113,6 +136,7 @@ importFrom(graph,nodeData)
 importFrom(graph,nodeDataDefaults)
 importFrom(graph,nodes)
 importFrom(graph,subGraph)
+importFrom(methods,as)
 importFrom(methods,coerce)
 importFrom(methods,show)
 useDynLib(openCyto,.registration = TRUE)

R/AllClasses.R

@@ -20,15 +20,14 @@
 #'
 #' Maintainer: Mike Jiang \email{wjiang2@@fhcrc.org}
 #' @name openCyto
-#' @docType package
 #' @title Hierarchical Gating Pipeline for flow cytometry data
 #' @keywords package
 #' @examples
 #' \dontrun{gatingTemplate('test.csv')}
 #' @seealso See \code{\link[openCyto]{gt_gating}}, 
 #' \code{\link{gate_flowclust_1d}}, 
 #' for an overview of gating functions.
-NULL
+"_PACKAGE"
 
 #' a class storing the gating method and population information in a graphNEL object
 #' 

R/fast_rlm.R

@@ -7,7 +7,8 @@
 #' @param x matrix with first column as weight (default can be 1s), the rest columns are predict variable
 #' @param y numeric vector as response 
 #' @param maxit maximum iterations
-#' @examples 
+#' @export
+#' @examples
 #' n <- 1e3
 #' x <- seq_len(n)
 #' y <- x * 2.5 - 1.3 + rnorm(n, sd = 30)

R/gating-functions.R

@@ -842,7 +842,7 @@ mindensity <- gate_mindensity
 #' @param gFunc the name of the 1d-gating function to be used for either dimension
 #' @param min a numeric vector that sets the lower bounds for data filtering
 #' @param max a numeric vector that sets the upper bounds for data filtering
-#' @param ... other arguments passed to \code{.find_peak} (e.g. 'num_peaks' and 'adjust'). see \link{tailgate}
+#' @param ... other arguments passed to \code{.find_peak} (e.g. 'num_peaks' and 'adjust').
 #' @return a \code{filters} that contains four rectangleGates
 #' @export 
 gate_quad_sequential <- function(fr, channels, gFunc, min = NULL, max = NULL, ...){

R/gating-methods.R

@@ -541,6 +541,7 @@ gt_gating.refGate <- function(x, y, ...) {
   .gating_refGate(x, y, ...)
 }
 
+#' @export
 gt_gating.dummyMethod <- function(x, y, ...) {
   #do nothing
 }

R/robust_m_estimator.R

@@ -1,4 +1,4 @@
-#' rewrite huber estimator
+# rewrite huber estimator
 robust_m_estimator <- function(x, sd)
 {
   stopifnot(sd != 0)