@@ -16,7 +16,7 @@

 #' }

 #' @importFrom flowWorkspace GatingSet transform

 #' @importFrom ncdfFlow read.ncdfFlowSet

-cytobank2GatingSet.default <- function(x, FCS){

+cytobank2GatingSet.default <- function(x, FCS, ...){

   g <- read.gatingML.cytobank(x)

   fs <- read.ncdfFlowSet(FCS)

   gs <- GatingSet(fs)

@@ -42,9 +42,11 @@ cytobankExperiment <- function(acs, exdir = tempfile()){

                         )

                    , class = "cytobankExperiment")

 }

+#' @rdname cytobank2GatingSet

 #' @export

 cytobank2GatingSet <- function(x, ...)UseMethod("cytobank2GatingSet")

 #' @importFrom flowWorkspace markernames<-

+#' @param ... other arguments

 #' @export

 #' @method cytobank2GatingSet cytobankExperiment

 #' @rdname cytobank2GatingSet

@@ -73,9 +75,10 @@ setOldClass("cytobankExperiment")

 #' @param x cytobankExperiment object

 #' @rdname cytobankExperiment

+#' @param ... not used

 #' @export

 #' @method print cytobankExperiment

-print.cytobankExperiment <- function(x){

+print.cytobankExperiment <- function(x, ...){

   exp <- x[["experiment"]]

   cat("cytobank Experiment: ", exp[["name"]],"\n");

   cat("gatingML File: ",x[["gatingML"]], "\n");

@@ -122,6 +125,7 @@ setMethod("markernames",

           })

 #' @rdname cytobankExperiment

+#' @param do.NULL,prefix not used

 #' @export

 setMethod("colnames",

           signature=signature(x="cytobankExperiment"),

@@ -148,7 +152,7 @@ get_panel_per_file <- function(ce){

 #' @export

 #' @method getTransformations cytobankExperiment

 #' @export getTransformations

-getTransformations.cytobankExperiment <- function(x){

+getTransformations.cytobankExperiment <- function(x, ...){

   chnls <- colnames(x)

   low.chnls <- tolower(chnls)

   scales <- x$experiment$scales

@@ -292,7 +292,7 @@ getCompensationMatrices.graphGML <- function(x){

 #' @importFrom methods extends

 #' @export

 #' @method getTransformations graphGML

-getTransformations.graphGML <- function(x){

+getTransformations.graphGML <- function(x, ...){

   trans <- x@graphData[["transformations"]]

   if(!is.null(trans)){

     chnls <- names(trans)

@@ -24,12 +24,11 @@ compare the counts to cytobank's exported csv so that the parsing result can be

 }

 \examples{

-xmlfile <- system.file("extdata/cytotrol_tcell_cytobank.xml", package = "CytoML")

-fcsFiles <- list.files(pattern = "CytoTrol", 

-        system.file("extdata", package = "flowWorkspaceData"), full = TRUE)

-gs <- cytobank2GatingSet(xmlfile, fcsFiles)

+acsfile <- system.file("extdata/cytobank_experiment.acs", package = "CytoML")

+ce <- cytobankExperiment(acsfile)

+gs <- cytobank2GatingSet(ce)

 ## verify the stats are correct

-statsfile <- system.file("extdata/cytotrol_tcell_cytobank_counts.csv", package = "CytoML")

+statsfile <- ce$attachments[1]

 dt_merged <- compare.counts(gs, statsfile, id.vars = "population", skip = "FCS Filename")

 all.equal(dt_merged[, count.x], dt_merged[, count.y], tol = 5e-4)

@@ -2,10 +2,13 @@

 % Please edit documentation in R/cytobank2GatingSet.R, R/cytobankExperiment.R

 \name{cytobank2GatingSet.default}

 \alias{cytobank2GatingSet.default}

+\alias{cytobank2GatingSet}

 \alias{cytobank2GatingSet.cytobankExperiment}

 \title{A wrapper that parse the gatingML and FCS files (or cytobankExperiment object) into GatingSet}

 \usage{

-\method{cytobank2GatingSet}{default}(x, FCS)

+\method{cytobank2GatingSet}{default}(x, FCS, ...)

+

+cytobank2GatingSet(x, ...)

 \method{cytobank2GatingSet}{cytobankExperiment}(x, ...)

 }

@@ -13,6 +16,8 @@

 \item{x}{the cytobankExperiment object or the full path of gatingML file}

 \item{FCS}{FCS files to be loaded}

+

+\item{...}{other arguments}

 }

 \value{

 a GatingSet

@@ -22,10 +27,12 @@ A wrapper that parse the gatingML and FCS files (or cytobankExperiment object) i

 }

 \examples{

 \dontrun{

-xmlfile <- system.file("extdata/cytotrol_tcell_cytobank.xml", package = "CytoML")

-fcsFiles <- list.files(pattern = "CytoTrol", 

-      system.file("extdata", package = "flowWorkspaceData"), full = TRUE)

-gs <- cytobank2GatingSet(xmlfile, fcsFiles)

-#plotGate(gs[[1]])

+acsfile <- system.file("extdata/cytobank_experiment.acs", package = "CytoML")

+ce <- cytobankExperiment(acsfile)

+xmlfile <- ce$gatingML

+fcsFiles <- list.files(ce$fcsdir, full.names = TRUE)

+gs <<- cytobank2GatingSet(xmlfile, fcsFiles)

+library(ggcyto)

+autoplot(gs[[1]])

 }

 }

@@ -14,7 +14,7 @@

 \usage{

 cytobankExperiment(acs, exdir = tempfile())

-\method{print}{cytobankExperiment}(x)

+\method{print}{cytobankExperiment}(x, ...)

 \method{getCompensationMatrices}{cytobankExperiment}(x)

@@ -23,7 +23,7 @@ cytobankExperiment(acs, exdir = tempfile())

 \S4method{colnames}{cytobankExperiment}(x, do.NULL = "missing",

   prefix = "missing")

-\method{getTransformations}{cytobankExperiment}(x)

+\method{getTransformations}{cytobankExperiment}(x, ...)

 \S4method{sampleNames}{cytobankExperiment}(object)

@@ -36,7 +36,11 @@ cytobankExperiment(acs, exdir = tempfile())

 \item{x}{cytobankExperiment object}

+\item{...}{not used}

+

 \item{object}{cytobankExperiment object}

+

+\item{do.NULL, prefix}{not used}

 }

 \value{

 cytobankExperiment object

@@ -4,7 +4,7 @@

 \alias{getTransformations.graphGML}

 \title{Extract transformations from graphGML object.}

 \usage{

-\method{getTransformations}{graphGML}(x)

+\method{getTransformations}{graphGML}(x, ...)

 }

 \arguments{

 \item{x}{graphGML}

@@ -7,7 +7,7 @@ This makefile requires GNU Make.

 endif

 CXX_STD = CXX11

-PKG_CPPFLAGS =-DROUT -I../inst/include/ @PKG_CPPFLAGS@ -Wno-deprecated-declarations

+PKG_CPPFLAGS =-DROUT -I../inst/include/ @PKG_CPPFLAGS@

 PKG_LIBS =`${R_HOME}/bin/Rscript -e "RProtoBufLib:::LdFlags();cat(' ');RcppParallel::RcppParallelLibs()"` @PKG_LIBS@ 

 USERDIR = ${R_PACKAGE_DIR}/lib${R_ARCH}