## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE, results = "markup", message = FALSE)

## ----findxml------------------------------------------------------------------
library(flowWorkspace)
path <- system.file("extdata",package="flowWorkspaceData");
wsfile <- list.files(path, pattern="A2004Analysis.xml", full = TRUE)

## ----openws,results='markup'--------------------------------------------------
library(CytoML)
ws <- open_flowjo_xml(wsfile)
ws

## ----getsamples-ws------------------------------------------------------------
fj_ws_get_samples(ws)

## ----getgroups----------------------------------------------------------------
fj_ws_get_sample_groups(ws)

## -----------------------------------------------------------------------------
sn <- "a2004_O1T2pb05i_A1_A01.fcs"
fj_ws_get_keywords(ws, sn)[1:5]

## ----parsews,message=FALSE, warning=FALSE-------------------------------------
gs <- flowjo_to_gatingset(ws,name = 1); #import the first group
#Lots of output here suppressed for the vignette.
gs

## ----sampleNames--------------------------------------------------------------
sampleNames(gs)

## ----parseGatingML, eval=FALSE------------------------------------------------
#  xmlfile <- system.file("extdata/cytotrol_tcell_cytobank.xml", package = "CytoML")
#  fcsFiles <- list.files(pattern = "CytoTrol", system.file("extdata", package = "flowWorkspaceData"), full = T)
#  gs1 <- parse.gatingML(xmlfile, fcsFiles)

## ----subset-------------------------------------------------------------------
gs[1]

## ----plotTree-----------------------------------------------------------------
plot(gs)

## ----gs_get_pop_paths-path-1--------------------------------------------------
gs_get_pop_paths(gs, path = 1)

## ----gs_get_pop_paths-path-full-----------------------------------------------
gs_get_pop_paths(gs, path = "full")

## ----gs_get_pop_paths-path-auto-----------------------------------------------
nodelist <- gs_get_pop_paths(gs, path = "auto")
nodelist

## ----gh_pop_get_gate----------------------------------------------------------
node <- nodelist[3]
g <- gs_pop_get_gate(gs, node)
g

## ----getStats-----------------------------------------------------------------
gs_pop_get_count_fast(gs)[1:10,]

## ----plotGate-nodeName--------------------------------------------------------
plotGate(gs, "pDC")

## ----annotate-----------------------------------------------------------------
d <- data.frame(sample=factor(c("sample 1", "sample 2")),treatment=factor(c("sample","control")) )
pd <- pData(gs)
pd <- cbind(pd,d)
pData(gs) <- pd
pData(gs)

## -----------------------------------------------------------------------------
subset(gs, treatment == "control")

## -----------------------------------------------------------------------------
fs <- gs_pop_get_data(gs)
class(fs)
nrow(fs[[1]])

## ----gh_pop_get_data-gs-------------------------------------------------------
fs <- gs_pop_get_data(gs, node)
nrow(fs[[1]])

## ----gh-----------------------------------------------------------------------
gh <- gs[[1]]
gh

## -----------------------------------------------------------------------------
head(gh_pop_compare_stats(gh))

## ----gh_plot_pop_count_cv-----------------------------------------------------
gh_plot_pop_count_cv(gh)

## -----------------------------------------------------------------------------
plotGate(gh)

## ----getInd-------------------------------------------------------------------
table(gh_pop_get_indices(gh,node))

## ----getCMAT------------------------------------------------------------------
C <- gh_get_compensations(gh);
C

## ----getTrans,results='markup'------------------------------------------------
T <- gh_get_transformations(gh)
names(T)
T[[1]]

## ----create gs----------------------------------------------------------------
library(flowCore)
data(GvHD)
#select raw flow data
fs <- GvHD[1:2]

## ----GatingSet constructor----------------------------------------------------
gs <- GatingSet(fs)

## ----compensate---------------------------------------------------------------
cfile <- system.file("extdata","compdata","compmatrix", package="flowCore")
comp.mat <- read.table(cfile, header=TRUE, skip=2, check.names = FALSE)
## create a compensation object 
comp <- compensation(comp.mat)
#compensate GatingSet
gs <- compensate(gs, comp)

## ----eval=FALSE---------------------------------------------------------------
#  gs <- compensate(gs, comp.list)

## ----user-transformation------------------------------------------------------
require(scales)
trans.func <- asinh
inv.func <- sinh
trans.obj <- trans_new("myAsinh", trans.func, inv.func)

## ----transform-build-in-------------------------------------------------------
trans.obj <- asinhtGml2_trans()
trans.obj

## ----transformerList----------------------------------------------------------
chnls <- colnames(fs)[3:6] 
transList <- transformerList(chnls, trans.obj)

## ----estimateLogicle----------------------------------------------------------
estimateLogicle(gs[[1]], chnls)

## ----transform-gs-------------------------------------------------------------
gs <- transform(gs, transList)
gs_get_pop_paths(gs) 

## ----add-rectGate-------------------------------------------------------------
rg <- rectangleGate("FSC-H"=c(200,400), "SSC-H"=c(250, 400), filterId="rectangle")
nodeID <- gs_pop_add(gs, rg)
nodeID
gs_get_pop_paths(gs)  

## ----add-quadGate-------------------------------------------------------------
qg <- quadGate("FL1-H"= 0.2, "FL2-H"= 0.4)
nodeIDs <- gs_pop_add(gs,qg,parent="rectangle")
nodeIDs 
gs_get_pop_paths(gs)

## ----add-boolGate-------------------------------------------------------------
bg <- booleanFilter(`CD15 FITC-CD45 PE+|CD15 FITC+CD45 PE-`)
bg
nodeID2 <- gs_pop_add(gs,bg,parent="rectangle")
nodeID2
gs_get_pop_paths(gs)

## ----plot-gh,eval=FALSE-------------------------------------------------------
#  plot(gs, bool=TRUE)

## ----recompute----------------------------------------------------------------
recompute(gs)

## ----plotGate-rect------------------------------------------------------------
plotGate(gs,"rectangle") #plot one Gate

## ----plotGate-multiple--------------------------------------------------------
plotGate(gs,gs_pop_get_children(gs[[1]], "rectangle")) 

## ----plotGate-gh-bool,eval=FALSE----------------------------------------------
#  plotGate(gs[[1]], bool=TRUE)

## ----rm-----------------------------------------------------------------------
Rm('rectangle', gs)
gs_get_pop_paths(gs)

## ----archive,eval=FALSE-------------------------------------------------------
#  tmp <- tempdir()
#  save_gs(gs,path = file.path(tmp,"my_gs"))
#  gs <- load_gs(file.path(tmp,"my_gs"))

## ----clone,eval=FALSE---------------------------------------------------------
#  gs_gs_cloned <- clone(gs)