@@ -1,4 +1,4 @@

-# Generated by roxygen2 (4.1.0): do not edit by hand

+# Generated by roxygen2: do not edit by hand

 S3method(extend,ellipsoidGate)

 S3method(extend,polygonGate)

@@ -234,8 +234,7 @@ gating.graphGML <- function(gt, gs, ...) {

     gateInfo <- gt_node[["gateInfo"]]

     this_gate <- gateInfo[["gate"]]

-#     if(popName == "PD-1(Histo)")

-#       browser()

+

     # transform bounds if applicable

     bound <- gateInfo[["bound"]]

@@ -248,7 +247,8 @@ gating.graphGML <- function(gt, gs, ...) {

       }

     }

-

+        # if(popName == "MDSC(gran-cd15+)")

+        #   browser()

     this_gate <- extend(this_gate,bound = bound)

     sn <- sampleNames(gs)

@@ -411,6 +411,7 @@ addGate <- function(gateInfo,flowEnv, g, popId, gateID){

 #'        rownames should be the channel names. colnames should be c("min", "max")

 #' @param data.range numeric matrix specifying the data limits of each channel. It is used to set the extended value of vertices and must has the same structure as 'bound'.

 #'        when it is not supplied, c(-.Machine$integer.max, - .Machine$integer.max) is used.

+#' @param limits character whether to plot in "extended" or "original" gate limits. Default is "original".

 #' @param ... other arguments

 #' @return a flowCore filter/gate

 #' @examples

@@ -422,7 +423,7 @@ addGate <- function(gateInfo,flowEnv, g, popId, gateID){

 #' bound <- matrix(c(100,3e3,100,3e3), byrow = TRUE, nrow = 2, dimnames = list(c("FSC-H", "SSC-H"), c("min", "max")))

 #' bound

 #' pg.extened <- extend(pg, bound, plot = TRUE)

-extend <- function(gate, bound, data.range = NULL, plot = FALSE)UseMethod("extend")

+extend <- function(gate, bound, data.range = NULL, plot = FALSE, limits = c("original", "extended"))UseMethod("extend")

 #' @export

 #' @S3method extend polygonGate

@@ -430,8 +431,8 @@ extend <- function(gate, bound, data.range = NULL, plot = FALSE)UseMethod("exten

 #' @param plot whether to plot the extended polygon.

 #' @importFrom flowCore polygonGate

 #' @importFrom graphics abline polygon text

-extend.polygonGate <- function(gate, bound, data.range = NULL, plot = FALSE){

-

+extend.polygonGate <- function(gate, bound, data.range = NULL, plot = FALSE, limits = c("original", "extended")){

+  limits <- match.arg(limits)

   #linear functions

   f.solve <- list(x = function(x, slope, x1, y1){

@@ -461,7 +462,7 @@ extend.polygonGate <- function(gate, bound, data.range = NULL, plot = FALSE){

   #this is a hack: We assume the polygon is convex

   #if not we turn the convcave into convex

   #to avoid the error

-  verts.orig <- verts.orig[chull(verts.orig),]

+  # verts.orig <- verts.orig[chull(verts.orig),]

   verts <- data.table(verts.orig)

   pname <- as.vector(parameters(gate))

@@ -539,7 +540,7 @@ extend.polygonGate <- function(gate, bound, data.range = NULL, plot = FALSE){

           }

-          c(point, id = i + 0.5)#jitter a positive ammount to break the tie with vert1

+          c(point, id = i + 0.1)#jitter a positive ammount to break the tie with vert1

         }

@@ -548,61 +549,96 @@ extend.polygonGate <- function(gate, bound, data.range = NULL, plot = FALSE){

-      this.intersect <- do.call(rbind, this.intersect)

+      this.intersect.df <- do.call(rbind, this.intersect)

+

       dim.flip <- ifelse(dim == "x", "y", "x")

 #       this.intersect <- this.intersect[order(this.intersect[[dim.flip]]),] #bottom to top/or left to right

-      nCount <- ifelse(is.null(this.intersect), 0, nrow(this.intersect))

+      nCount <- ifelse(is.null(this.intersect.df), 0, nrow(this.intersect.df))

       if(nCount > 0){

-        if(nCount!= 2)

-          stop("Unsupported number of intersected points with ", bn, " boundary on ", dim, " axis: ", nCount)

-

-        verts[, id := 1:nVerts]#record the id before insertion

-        this.intersect <- as.data.table(this.intersect)

-

-        #insert the intersect points

-        verts <- rbindlist(list(verts, this.intersect))

-        verts <- verts[order(id),]

-

-        #remove off-bound points

-        if(bn == "min")

-          ind <- verts[, dim, with = FALSE] < intersect.coord

-        else

-          ind <- verts[, dim, with = FALSE] > intersect.coord

-        ind <- as.vector(ind)

-        verts <- verts[!ind, ]

-

-        #add extended points

-        this.extend <- this.intersect

-        this.extend[, dim] <- data.range[dim, bn]

-

-        #sort by the Id

-        this.extend[, is.smaller:= order(id) == 1]

-        #check if head-tail node situation

-

-        this.extend[, is.tail := id == verts[,max(id)]]

-        this.extend[, is.head := id == verts[,min(id)]]

-

-        nhead <- sum(this.extend[, is.head])

-        ntail <- sum(this.extend[, is.tail])

-

-

-        if(nhead == 0||ntail == 0){#two consecutive points

-          this.extend[is.smaller == TRUE, id := id + 0.1]

-          this.extend[is.smaller == FALSE, id := this.extend[is.smaller == TRUE, id] + 0.1]

-        }else if(nhead == 1 && ntail == 1){

-          #deal with head-tail points

-          this.extend[is.smaller == TRUE, id := id - 0.1]

-          this.extend[is.smaller == FALSE, id := this.extend[is.smaller == TRUE, id] - 0.1]

-        }else

-          stop("Incorrect number of head and tail points!")

+        if(nCount %% 2 != 0)

+          stop("uneven number of intersected points with ", bn, " boundary on ", dim, " axis: ", nCount)

+      verts[, id := 1:nVerts]#record the id before insertion

+      verts[, key := paste0(x,",", y)] # generate key for the comparsion to intersected points later on

+

+      #reset id for the duplicated intersects so that they won't cause chaos for the ordering later on

+      this.intersect.df <- as.data.table(this.intersect.df)

+      this.intersect.df[, key := paste0(x,",", y)]

+      this.intersect.df[, id := min(id), by = key]

+      #order by dim so that extension to pairs follows the order

+      setorderv(this.intersect.df, dim.flip)

+      inserted.ids <- NULL

+      #loop through each pair of extended points

+      for(i in seq_len(nCount/2)){

+          j <- 2 * i

+          # browser()

+          this.intersect <- this.intersect.df[(j -1):j, ]

+

+          # this.intersect <- as.data.table(this.intersect)

+

+          #remove the original edge points that overlap with intersect points

+          #but keep the intersected points inserted previously

+          #nchar(id) : length of significant digits

+          #== 1: original points

+          #== 2: intersected

+          #== 4: extended

+          # verts <- verts[!(key %in% this.intersect[, key] && nchar(id) == 1), ]

+          verts <- verts[!(key %in% this.intersect[, key]), ]

+

+

+

+          #keep track of id that has been inserted repeatly

+          #so that the duplicated intersects can be removed later

+          #otherwise, it could mess up the already removed off-bound points

+          dup.id <- this.intersect[id %in% inserted.ids, id]

+          inserted.ids <- unique(c(inserted.ids, this.intersect[, id]))

+          #insert the intersect points

+          verts <- rbindlist(list(verts, this.intersect))

+          verts <- verts[order(id),]

+

+          #remove off-bound points between the two intersected points

+          vals.dim <- verts[, dim, with = FALSE]

+          vals.dim.flip <- verts[, dim.flip, with = FALSE]

+          rng.dim.flip  <- range(this.intersect[[dim.flip]])

+          ind.between <- vals.dim.flip <= rng.dim.flip[2] & vals.dim.flip >= rng.dim.flip[1]

+          if(bn == "min")

+            ind <- vals.dim < intersect.coord & ind.between

+          else

+            ind <- vals.dim > intersect.coord & ind.between

+          ind <- as.vector(ind)

+          verts <- verts[!ind, ]

+

+

+

+          #add extended points

+          this.extend <- this.intersect

+          this.extend[, dim] <- data.range[dim, bn]

+          this.extend[, key := paste0(x,",", y)]#update key

+

+          #sort by the Id

+          this.extend[, is.smaller:= order(id) == 1]

+          #check if head-tail node situation

+          # by cal the distance between two points

+          this.extend[, order := match(id, verts[,id])]

+          dist <- abs(diff(this.extend[, order]))

+          if(dist == 1){#two consecutive points

+            this.extend[is.smaller == TRUE, id := id + 0.01]

+            this.extend[is.smaller == FALSE, id := this.extend[is.smaller == TRUE, id] + 0.01]

+          }else{

+            #deal with head-tail points

+            this.extend[is.smaller == TRUE, id := id - 0.01]

+            this.extend[is.smaller == FALSE, id := this.extend[is.smaller == TRUE, id] - 0.01]

+          }

+          # browser()

+          this.extend[, is.smaller := NULL]

+          this.extend[, order := NULL]

+          #remove dup id

+          verts <- verts[!id%in%dup.id, ]

-        this.extend[, is.smaller := NULL]

-        this.extend[, is.head := NULL]

-        this.extend[, is.tail := NULL]

+          verts <- rbindlist(list(verts, this.extend))

+          verts <- verts[order(id),]

-        verts <- rbindlist(list(verts, this.extend))

-        verts <- verts[order(id),]

+        }

       }

@@ -610,16 +646,19 @@ extend.polygonGate <- function(gate, bound, data.range = NULL, plot = FALSE){

   }

-

+# browser()

   if(plot){

-    plot(type = "n", x = verts.orig[,1], y = verts.orig[,2])

+    if(limits == "extended")

+      plot(type = "n", x = verts[[1]], y = verts[[2]])

+    else

+      plot(type = "n", x = verts.orig[,1], y = verts.orig[,2])

     polygon(verts.orig, lwd =  4, border = rgb(0, 0, 0,0.5))

     # points(verts.orig, col = "red")

     # points(t(as.data.frame(colMeans(verts.orig))), col = "red")

-    abline(v = bound[1,], lty = "dashed", col = "red")

-    abline(h = bound[2,], lty = "dashed", col = "red")

+    # abline(v = bound[1,], lty = "dashed", col = "red")

+    # abline(h = bound[2,], lty = "dashed", col = "red")

     text(verts, labels = verts[, id], col = "red")

     # points(intersect.points[, c(axis.names)], col = "blue")

     polygon(verts, lty = "dotted", border = "green", lwd = 3)

@@ -26,6 +26,6 @@ test_that("gatingML-cytobank exporting: cytotrol tcell",{

   stats.new <- getPopStats(gs1)

   stats <- merge(stats.orig, stats.new, by = c("name", "Population", "Parent"))

-  expect_equal(stats[, Count.x/ParentCount.x], stats[, Count.y/ParentCount.y], tol = 7e-3)

+  expect_equal(stats[, Count.x/ParentCount.x], stats[, Count.y/ParentCount.y])

 })

\ No newline at end of file

new file mode 100644

@@ -0,0 +1,90 @@

+chnls <- c("FSC-H","SSC-H")

+data.range <- data.frame(min = c(-1, -1), max = c(4e3, 4e3), row.names = chnls)

+sqrcut <- matrix(c(300, 50

+                   ,300, 300

+                   , 600, 300

+                   , 600, 50)

+                 , byrow = TRUE, nrow=4

+                 , dimnames = list(NULL, chnls))

+pg <- polygonGate(filterId="nonDebris", sqrcut)

+

+test_that("extend.polygonGate: y axis",{

+

+  bound <- matrix(c(100,3e3

+                    ,100,3e3)

+                  , byrow = TRUE, nrow = 2

+                  , dimnames = list(chnls, c("min", "max")))

+  pg.extened <- extend(pg, bound)

+  # paste(as.vector(pg.extened@boundaries), collapse = ",")

+  expectRes <- matrix(c(600,-2147483647

+                        ,300,-2147483647

+                        ,300,100

+                        ,300,300

+                        ,600,300

+                        ,600,100

+                       )

+                     ,byrow = TRUE,nrow=6)

+  expect_equivalent(pg.extened@boundaries, expectRes)

+

+})

+

+test_that("extend.polygonGate: both x and y axis",{

+  bound <- matrix(c(400,3e3

+                    ,100,3e3)

+                  , byrow = TRUE, nrow = 2

+                  , dimnames = list(chnls, c("min", "max")))

+  pg.extened <- extend(pg, bound)

+

+

+  expectRes <- matrix(c(600,-2147483647,-2147483647,-2147483647,400,600,600,-2147483647,-2147483647,100,300,300,300,100), nrow = 7)

+

+  expect_equivalent(pg.extened@boundaries, expectRes)

+

+})

+

+test_that("extend.polygonGate: concave on left with data.range",{

+  sqrcut <- matrix(c(300, 50

+                     , 450, 150

+                     ,300, 300

+                     , 600, 300

+                     , 600, 50)

+                   , byrow = TRUE, nrow=5

+                   , dimnames = list(NULL, chnls))

+  pg <- polygonGate(filterId="nonDebris", sqrcut)

+  bound <- matrix(c(400,3e3

+                    ,10,3e3)

+                  , byrow = TRUE, nrow = 2

+                  , dimnames = list(chnls, c("min", "max")))

+  pg.extened <- extend(pg, bound, data.range = data.range)

+

+  expectRes <- matrix(c(-1,-1,400,450,400,-1,-1,400,600,600,400,50,116.666666666667,116.666666666667,150,200,200,300,300,300,50,50)

+                      , nrow = 11)

+

+  expect_equivalent(pg.extened@boundaries, expectRes)

+

+})

+

+test_that("extend.polygonGate: concave on left& bottom with data.range",{

+  sqrcut <- matrix(c(300, 50

+                     , 450, 150

+                     ,300, 300

+                     , 600, 300

+                     , 600, 50

+                     , 550,100

+                     , 500,50

+                     , 450,60)

+                   , byrow = TRUE, nrow=8

+                   , dimnames = list(NULL, chnls))

+  pg <- polygonGate(filterId="nonDebris", sqrcut)

+  bound <- matrix(c(400,3e3

+                    ,100,3e3)

+                  , byrow = TRUE, nrow = 2

+                  , dimnames = list(chnls, c("min", "max")))

+  pg.extened <- extend(pg, bound, data.range = data.range)

+

+  expectRes <- matrix(c(-1,-1,-1,400,450,400,-1,-1,400,600,600,600,550,-1,100,116.666666666667,116.666666666667,150,200,200,300,300,300,100,-1,-1)

+                      , nrow = 13)

+

+  expect_equivalent(pg.extened@boundaries, expectRes)

+

+})

\ No newline at end of file

@@ -1,4 +1,4 @@

-% Generated by roxygen2 (4.1.0): do not edit by hand

+% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/GatingSet2cytobank.R

 \name{GatingSet2cytobank}

 \alias{GatingSet2cytobank}

@@ -43,5 +43,7 @@ Rm("CD8", gs)

 #output to cytobank

 outFile <- tempfile(fileext = ".xml")

 GatingSet2cytobank(gs, outFile) #type by default is 'cytobank'

+

+

 }

@@ -1,4 +1,4 @@

-% Generated by roxygen2 (4.1.0): do not edit by hand

+% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/GatingSet2flowJo.R

 \name{GatingSet2flowJo}

 \alias{GatingSet2flowJo}

@@ -29,5 +29,7 @@ gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE))

 #output to flowJo

 outFile <- tempfile(fileext = ".wsp")

 GatingSet2flowJo(gs, outFile)

+

+

 }

@@ -1,4 +1,4 @@

-% Generated by roxygen2 (4.1.0): do not edit by hand

+% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/GatingSet2cytobank.R

 \name{addCustomInfo}

 \alias{addCustomInfo}

@@ -1,10 +1,10 @@

-% Generated by roxygen2 (4.1.0): do not edit by hand

+% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/cytobank2GatingSet.R

 \name{compare.counts}

 \alias{compare.counts}

 \title{compare the counts to cytobank's exported csv so that the parsing result can be verified.}

 \usage{

-compare.counts(gs, file, id.vars = c("FCS Filename", "population"))

+\method{compare}{counts}(gs, file, id.vars = c("FCS Filename", "population"))

 }

 \arguments{

 \item{gs}{parsed GatingSet}

@@ -20,6 +20,7 @@ a data.table (in long format) that contains the counts from openCyto and Cytoban

 compare the counts to cytobank's exported csv so that the parsing result can be verified.

 }

 \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)

@@ -27,5 +28,6 @@ gs <- cytobank2GatingSet(xmlfile, fcsFiles)

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

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

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

+

 }

@@ -1,4 +1,4 @@

-% Generated by roxygen2 (4.1.0): do not edit by hand

+% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/graphGML_methods.R

 \docType{methods}

 \name{compensate,GatingSet,graphGML-method}

@@ -1,4 +1,4 @@

-% Generated by roxygen2 (4.1.0): do not edit by hand

+% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/read.gatingML.cytobank.R

 \name{constructTree}

 \alias{constructTree}

@@ -1,4 +1,4 @@

-% Generated by roxygen2 (4.1.0): do not edit by hand

+% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/cytobank2GatingSet.R

 \name{cytobank2GatingSet}

 \alias{cytobank2GatingSet}

@@ -18,9 +18,11 @@ a GatingSet

 A wrapper that parse the gatingML and FCS files into GatingSet

 }

 \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)

 #plotGate(gs[[1]])

+

 }

@@ -1,4 +1,4 @@

-% Generated by roxygen2 (4.1.0): do not edit by hand

+% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/read.gatingML.cytobank.R

 \name{extend}

 \alias{extend}

@@ -7,9 +7,11 @@

 \alias{extend.rectangleGate}

 \title{extend the gate to the minimum and maximum limit of both dimensions based on the bounding information.}

 \usage{

-extend(gate, bound, data.range = NULL, plot = FALSE)

+extend(gate, bound, data.range = NULL, plot = FALSE,

+  limits = c("original", "extended"))

-\method{extend}{polygonGate}(gate, bound, data.range = NULL, plot = FALSE)

+\method{extend}{polygonGate}(gate, bound, data.range = NULL, plot = FALSE,

+  limits = c("original", "extended"))

 \method{extend}{rectangleGate}(gate, ...)

@@ -26,6 +28,8 @@ when it is not supplied, c(-.Machine$integer.max, - .Machine$integer.max) is use

 \item{plot}{whether to plot the extended polygon.}

+\item{limits}{character whether to plot in "extended" or "original" gate limits. Default is "original".}

+

 \item{...}{other arguments}

 }

 \value{

@@ -1,4 +1,4 @@

-% Generated by roxygen2 (4.1.0): do not edit by hand

+% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/graphGML_methods.R

 \docType{methods}

 \name{gating,graphGML,GatingSet-method}

@@ -1,4 +1,4 @@

-% Generated by roxygen2 (4.1.0): do not edit by hand

+% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/graphGML_methods.R

 \docType{methods}

 \name{getChildren,graphGML,character-method}

@@ -1,4 +1,4 @@

-% Generated by roxygen2 (4.1.0): do not edit by hand

+% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/graphGML_methods.R

 \docType{methods}

 \name{getCompensationMatrices,graphGML-method}

@@ -1,4 +1,4 @@

-% Generated by roxygen2 (4.1.0): do not edit by hand

+% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/graphGML_methods.R

 \docType{methods}

 \name{getGate,graphGML,character-method}

@@ -1,4 +1,4 @@

-% Generated by roxygen2 (4.1.0): do not edit by hand

+% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/graphGML_methods.R

 \docType{methods}

 \name{getNodes,graphGML-method}

@@ -1,4 +1,4 @@

-% Generated by roxygen2 (4.1.0): do not edit by hand

+% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/graphGML_methods.R

 \docType{methods}

 \name{getParent,graphGML,character-method}

@@ -1,4 +1,4 @@

-% Generated by roxygen2 (4.1.0): do not edit by hand

+% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/graphGML_methods.R

 \docType{methods}

 \name{getTransformations,graphGML-method}

@@ -1,4 +1,4 @@

-% Generated by roxygen2 (4.1.0): do not edit by hand

+% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/read.gatingML.cytobank.R

 \docType{class}

 \name{graphGML-class}

@@ -1,4 +1,4 @@

-% Generated by roxygen2 (4.1.0): do not edit by hand

+% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/read.gatingML.cytobank.R

 \name{matchPath}

 \alias{matchPath}

@@ -1,4 +1,4 @@

-% Generated by roxygen2 (4.1.0): do not edit by hand

+% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/read.gatingML.cytobank.R

 \name{parse.gateInfo}

 \alias{parse.gateInfo}

@@ -1,4 +1,4 @@

-% Generated by roxygen2 (4.1.0): do not edit by hand

+% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/graphGML_methods.R

 \docType{methods}

 \name{plot,graphGML,missing-method}

@@ -25,5 +25,6 @@ The node with dotted order represents the population that has tailored gates (sa

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

 g <- read.gatingML.cytobank(xmlfile)

 plot(g)

+

 }

@@ -1,4 +1,4 @@

-% Generated by roxygen2 (4.1.0): do not edit by hand

+% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/read.gatingML.cytobank.R

 \name{read.gatingML.cytobank}

 \alias{read.gatingML.cytobank}

@@ -1,4 +1,4 @@

-% Generated by roxygen2 (4.1.0): do not edit by hand

+% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/graphGML_methods.R

 \docType{methods}

 \name{show,graphGML-method}