Browse code

update docs

mikejiang authored on 13/07/2017 20:17:32
Showing 25 changed files

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@@ -36,7 +36,7 @@ Suggests:
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 LinkingTo: Rcpp, flowWorkspace, BH(>= 1.62.0-1), RProtoBufLib
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 VignetteBuilder: knitr
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 SystemRequirements: xml2, GNU make, C++11
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-RoxygenNote: 5.0.1
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+RoxygenNote: 6.0.1
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 Collate:
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     'GatingSet2cytobank.R'
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     'GatingSet2flowJo.R'
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@@ -50,4 +50,3 @@ GatingSet2cytobank(gs, outFile) #type by default is 'cytobank'
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 }
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-
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@@ -32,4 +32,3 @@ GatingSet2flowJo(gs, outFile)
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 }
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-
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@@ -25,4 +25,3 @@ XML root node
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 \description{
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 add customInfo nodes to each gate node and add BooleanAndGates
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 }
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-
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@@ -30,4 +30,3 @@ dt_merged <- compare.counts(gs, statsfile, id.vars = "population")
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 all.equal(dt_merged[, count.x], dt_merged[, count.y], tol = 5e-4)
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 }
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-
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@@ -20,4 +20,3 @@ compensated GatingSet
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 \description{
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 compensate a GatingSet based on the compensation information stored in graphGML object
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 }
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-
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@@ -17,4 +17,3 @@ a graphNEL represent the population tree. The gate and population name are store
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 \description{
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 Reconstruct the population tree from the GateSets
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 }
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-
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@@ -25,4 +25,3 @@ gs <- cytobank2GatingSet(xmlfile, fcsFiles)
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 #plotGate(gs[[1]])
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 }
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-
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@@ -3,10 +3,10 @@
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 \docType{class}
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 \name{divaWorkspace-class}
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 \alias{divaWorkspace-class}
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-\alias{getSampleGroups,divaWorkspace-method}
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 \alias{getSamples,divaWorkspace-method}
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-\alias{parseWorkspace,divaWorkspace-method}
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+\alias{getSampleGroups,divaWorkspace-method}
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 \alias{show,divaWorkspace-method}
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+\alias{parseWorkspace,divaWorkspace-method}
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 \title{divaWorkspace class
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 Inherited from \link{flowJoWorkspace-class}}
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 \usage{
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@@ -22,4 +22,3 @@ Inherited from \link{flowJoWorkspace-class}}
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 divaWorkspace class
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 Inherited from \link{flowJoWorkspace-class}
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 }
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-
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@@ -2,9 +2,9 @@
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 % Please edit documentation in R/read.gatingML.cytobank.R
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 \name{extend}
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 \alias{extend}
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-\alias{extend.ellipsoidGate}
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 \alias{extend.polygonGate}
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 \alias{extend.rectangleGate}
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+\alias{extend.ellipsoidGate}
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 \title{extend the gate to the minimum and maximum limit of both dimensions based on the bounding information.}
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 \usage{
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 extend(gate, bound, data.range = NULL, plot = FALSE,
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@@ -56,4 +56,3 @@ bound <- matrix(c(100,3e3,100,3e3), byrow = TRUE, nrow = 2, dimnames = list(c("F
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 bound
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 pg.extened <- extend(pg, bound, plot = TRUE)
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 }
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-
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@@ -20,4 +20,3 @@ Nothing. As the side effect, gates generated by gating methods are saved in \cod
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 \description{
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 It applies the gates to the GatingSet based on the population tree described in graphGML.
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 }
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-
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@@ -24,4 +24,3 @@ g <- read.gatingML.cytobank(xmlfile)
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 getChildren(g, "GateSet_722326")
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 getParent(g, "GateSet_722326")
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 }
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-
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@@ -16,4 +16,3 @@ compensation object or "FCS" when compensation comes from FCS keywords
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 \description{
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 Extract compensation from graphGML object.
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 }
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-
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@@ -18,4 +18,3 @@ the gate information associated with the node
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 \description{
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 get gate from the node
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 }
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-
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@@ -29,4 +29,3 @@ g <- read.gatingML.cytobank(xmlfile)
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 getNodes(g)
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 getNodes(g, only.names = FALSE)
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 }
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-
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@@ -18,4 +18,3 @@ a graphNEL node
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 \description{
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 get parent nodes
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 }
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-
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@@ -16,4 +16,3 @@ transformerList object
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 \description{
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 Extract transformations from graphGML object.
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 }
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-
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@@ -11,4 +11,3 @@ associated with each node as nodeData. Compensation and transformations are stor
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 \details{
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 The class simply extends the graphNEL class and exists for the purpose of method dispatching.
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 }
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-
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@@ -19,4 +19,3 @@ TRUE if path is found, FALSE if not path is matched.
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 \description{
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 Given the leaf node, try to find out if a collection of nodes can be matched to a path in a graph(tree) by the bottom-up searching
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 }
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-
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@@ -33,4 +33,3 @@ getNodes(gs)
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 plotGate(gs[[1]])
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 }
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 }
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-
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@@ -18,4 +18,3 @@ a data.frame that contains three columns: id (gateId), name (gate name), fcs (fc
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 Fcs filename and gate name stored in 'custom_info' element are beyong the scope of
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 the gatingML standard and thus not covered by the default 'read.gatingML'.
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 }
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-
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@@ -27,4 +27,3 @@ g <- read.gatingML.cytobank(xmlfile)
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 plot(g)
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 }
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-
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@@ -25,4 +25,3 @@ xml <- system.file("extdata/cytotrol_tcell_cytobank.xml", package = "CytoML")
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 g <- read.gatingML.cytobank(xml) #parse the population tree
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 #plot(g) #visualize it
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 }
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-
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@@ -21,4 +21,3 @@ It is for internal use by the diva parser
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 set.count.xml(gh, "CD3", 10000)
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 }
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 }
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-
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@@ -16,4 +16,3 @@ nothing
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 \description{
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 show method for graphGML
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 }
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-