diff --git a/NAMESPACE b/NAMESPACE
index 4d46e45..0309d38 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -46,5 +46,6 @@ export(setServer)
 export(updateExperiment)
 export(updateGate)
 export(updateGateFamily)
+export(updateScaleSets)
 export(uploadAttachment)
 export(uploadFcsFile)
diff --git a/R/convertFlowCore.R b/R/convertFlowCore.R
index e7d327a..e03c4ef 100644
--- a/R/convertFlowCore.R
+++ b/R/convertFlowCore.R
@@ -174,3 +174,27 @@ convertFromFlowCore <- function (flowObject, scaleSet, name=NULL) {
     }
   )
 }
+
+# this is a pretty annoying function
+# appendToScaleSet <- function (tl) {
+#   browser()
+#   scales = c()
+#   channels = names(tl@transforms)
+#   mapply(
+#     function (tf) {
+
+#       tf@f
+#       _scale = list(channelName = tf@input)
+#     },
+#     tl@transforms
+#   )
+#   list(
+#     `_id` = "foo",
+#     experimentId = "bar",
+#     name = tl@transformationId,
+#     scales = scales,
+#   )
+# }
+
+scaleSetToTransformList <- function (scaleSet) {
+}
diff --git a/R/updateScaleSets.R b/R/updateScaleSets.R
new file mode 100644
index 0000000..d423212
--- /dev/null
+++ b/R/updateScaleSets.R
@@ -0,0 +1,21 @@
+#' Update scale set
+#'
+#' Updates a scale set.
+#'
+#' @param experimentId ID of experiment.
+#' @param properties Properties to set on the gate.
+#' @param params Optional query parameters.
+#' @export
+#' @examples
+#' \dontrun{
+#' updateScaleSets(experimentId, gid, list("name" = "new gate name"))
+#' }
+
+updateScaleSets = function(experimentId, gid, properties = list(), params = list()) {
+  checkDefined(experimentId)
+  checkDefined(gid)
+  experimentId = lookupByName("experiments", experimentId)
+  body = jsonlite::toJSON(properties, null = "null")
+  base = paste("experiments", experimentId, "scalesets", sep = "/")
+  basePatch(url, body, params)
+}
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 9a8d9b9..ff184c0 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -33,6 +33,7 @@ reference:
   - title: Scales
     contents:
       - getScaleSets
+      - updateScaleSets
       - applyScale
 
   - title: Compensations
diff --git a/man/covarToParameters.Rd b/man/covarToParameters.Rd
new file mode 100644
index 0000000..5fb6b05
--- /dev/null
+++ b/man/covarToParameters.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/covarToParameters.R
+\name{covarToParameters}
+\alias{covarToParameters}
+\title{Covert covariance matrix to ellipse parameters}
+\usage{
+covarToParameters(covar)
+}
+\arguments{
+\item{covar}{Covariance matrix}
+}
+\description{
+Returns list("major" = major, "minor" = minor, "angle" = angle)
+}
diff --git a/man/downloadFcsFiles.Rd b/man/downloadFcsFiles.Rd
index 80d2f34..80c27e3 100644
--- a/man/downloadFcsFiles.Rd
+++ b/man/downloadFcsFiles.Rd
@@ -31,8 +31,8 @@ downloadFcsFiles(
 
 \item{overwrite}{[Logical] Allows a destination file to be overwritten.}
 
-\item{fcsFileIds}{[Array<String>] Optional. Defaults to returning all files
-in the experiment.}
+\item{fcsFileIds}{[Array<String>] Optional. Defaults to returning all
+non-control files in the experiment.}
 
 \item{populationIds}{[Array<String>] Optional. If provided, only events from
 these populations will be included in the output files. Defaults to ungated.}
@@ -46,24 +46,24 @@ numerical values will be the compensated values. For FCS format, the
 numerical values will be unchanged, but the file header will contain the
 compensation as the spill string (file-internal compensation).}
 
-\item{preSubsampleN}{[Integer] Randomly subsample the file to contain this many events
-before gating.}
+\item{preSubsampleN}{[Integer] Randomly subsample the file to contain this
+many events before gating.}
 
-\item{preSubsampleP}{[Numeric] Randomly subsample the file to contain this percent of
-events (0 to 1) before gating.}
+\item{preSubsampleP}{[Numeric] Randomly subsample the file to contain this
+percent of events (0 to 1) before gating.}
 
-\item{seed}{[Numeric] Seed for random number generator used for subsampling. Use for
-deterministic (reproducible) subsampling. If omitted, a pseudo-random value
-is used.}
+\item{seed}{[Numeric] Seed for random number generator used for
+subsampling. Use for deterministic (reproducible) subsampling. If omitted, a
+pseudo-random value is used.}
 
-\item{filenameTemplate}{[String]    Tokenized template to dynamically name each
-file in the resulting archive, like "{file.name}-{population.name}"}
+\item{filenameTemplate}{[String]    Tokenized template to dynamically name
+each file in the resulting archive, like "{file.name}-{population.name}"}
 
-\item{postSubSampleN}{[Integer] Randomly subsample the file to contain this many events
-after gating.}
+\item{postSubSampleN}{[Integer] Randomly subsample the file to contain this
+many events after gating.}
 
-\item{postSubSampleP}{[Numeric] Randomly subsample the file to contain this percent of
-events (0 to 1) after gating.}
+\item{postSubSampleP}{[Numeric] Randomly subsample the file to contain this
+percent of events (0 to 1) after gating.}
 }
 \description{
 Downloads multiple files bundled into a ZIP archive.
diff --git a/man/getFcsFiles.Rd b/man/getFcsFiles.Rd
index 94a2633..cc21009 100644
--- a/man/getFcsFiles.Rd
+++ b/man/getFcsFiles.Rd
@@ -12,8 +12,10 @@ getFcsFiles(experimentId, params = list())
 \item{params}{Optional query parameters.}
 }
 \description{
-Retrieves the list of FCS files in an experiment. This does not download the
-FCS files themselves; this only returns information about the FCS files.
+Retrieves the list of FCS files in an experiment. This does not download
+the FCS files themselves; this only returns information about the FCS files.
+Only returns non-control FCS files unless "includeControls"=T is passed in
+params.
 }
 \examples{
 \dontrun{
diff --git a/man/updateScaleSets.Rd b/man/updateScaleSets.Rd
new file mode 100644
index 0000000..c66e213
--- /dev/null
+++ b/man/updateScaleSets.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/updateScaleSets.R
+\name{updateScaleSets}
+\alias{updateScaleSets}
+\title{Update scale set}
+\usage{
+updateScaleSets(experimentId, gid, properties = list(), params = list())
+}
+\arguments{
+\item{experimentId}{ID of experiment.}
+
+\item{properties}{Properties to set on the gate.}
+
+\item{params}{Optional query parameters.}
+}
+\description{
+Updates a scale set.
+}
+\examples{
+\dontrun{
+updateScaleSets(experimentId, gid, list("name" = "new gate name"))
+}
+}
diff --git a/tests/testthat/test-convertFlowCore.R b/tests/testthat/test-convertFlowCore.R
index a02b3aa..5b6ceb6 100644
--- a/tests/testthat/test-convertFlowCore.R
+++ b/tests/testthat/test-convertFlowCore.R
@@ -5,173 +5,182 @@ capture_warnings({
   library("flowDensity")
 })
 
-  test_that("rectangle gate is converted to flowCore", {
-    content = '{"__v":0,"experimentId":"591a3b441d725115208a6fda","model":{"label":[150440.453608247,202688.886597938],"rectangle":{"y2":214399.74226804124,"x2":182870.51546391752,"y1":190978.03092783503,"x1":118010.39175257733},"locked":false},"gid":"592640a5a6a1d6256ec9b08a","xChannel":"FSC-A","type":"RectangleGate","name":"my gate","parentPopulationId":null,"yChannel":"FSC-W","_id":"592640aa298f1480900e10e4","tailoredPerFile":false,"id":"592640aa298f1480900e10e4"}'
-    gate <- jsonlite::fromJSON(content)
-
-    flowGate <- convertToFlowCore(gate)
-    expect_equal(flowGate@filterId, "my gate")
-    expect_true(flowGate@min[1] == gate$model$rectangle$x1)
-    expect_true(flowGate@min[2] == gate$model$rectangle$y1)
-    expect_true(flowGate@max[1] == gate$model$rectangle$x2)
-    expect_true(flowGate@max[2] == gate$model$rectangle$y2)
-  })
-
-  test_that("ellipse gate is converted to flowCore", {
-    content = '{"__v":0,"experimentId":"591a3b441d725115208a6fda","model":{"label":[106299.536082474,85580.3298969073],"ellipse":{"angle":0.7039529178881421,"major":166096.6309940297,"minor":102655.51977381333,"center":[106299.53608247427,85580.32989690728]},"locked":false},"gid":"59289ff2461f1fd925fca4ff","xChannel":"FSC-A","type":"EllipseGate","name":"my gate","parentPopulationId":null,"yChannel":"FSC-W","_id":"59289ff59989cc7704ada3c0","tailoredPerFile":false,"id":"59289ff59989cc7704ada3c0"}'
-    gate <- jsonlite::fromJSON(content)
-
-    flowGate <- convertToFlowCore(gate)
-    expect_equal(flowGate@filterId, "my gate")
-    expect_equal(flowGate@mean[1], gate$model$ellipse$center[1], tolerance=0.001, check.names=F)
-    expect_equal(flowGate@mean[2], gate$model$ellipse$center[2], tolerance=0.001, check.names=F)
-  })
-
-  test_that("polygon gate is converted to flowCore", {
-    content='{"__v":0,"experimentId":"591a3b441d725115208a6fda","model":{"label":[150440.453608247,202688.886597938],"polygon":{"vertices":[[37836.07,971.51],[1588732.12,154.646],[8139.405,664.78],[9441.949,781.32]]},"locked":false},"gid":"592640a5a6a1d6256ec9b08a","xChannel":"FSC-A","type":"PolygonGate","name":"my gate","parentPopulationId":null,"yChannel":"FSC-W","_id":"592640aa298f1480900e10e4","tailoredPerFile":false,"id":"592640aa298f1480900e10e4"}'
-    gate <- jsonlite::fromJSON(content)
-
-    flowGate <- convertToFlowCore(gate)
-    expect_equal(flowGate@filterId, "my gate")
-    expect_true(all(flowGate@boundaries == gate$model$polygon$vertices))
-  })
-
- test_that("flowDensity is converted to polygonGate", {
-   # given
-   content='{"__v":0,"experimentId":"5d2f8b4b21fd0676fb3a6a70","model":{"label":[150440.453608247,202688.886597938],"polygon":{"vertices":[[222400,94720],[216128,85568],[201344,77696],[194752,75264],[19584,67904],[19072,68864],[20800,75648],[25920,93312],[37184,101120],[51648,104576],[82816,109824],[95040,111488],[107712,112512],[144384,114304],[172224,114240],[176640,113920],[190336,112512],[197632,111040],[211072,104448],[222400,94720]]},"locked":false},"gid":"592640a5a6a1d6256ec9b08a","xChannel":"FSC-A","type":"PolygonGate","name":"converted gate","parentPopulationId":null,"yChannel":"FSC-W","_id":"592640aa298f1480900e10e4","tailoredPerFile":false,"id":"592640aa298f1480900e10e4"}'
-   gate <- jsonlite::fromJSON(content)
-   # createPolygonGate is stubbed to avoid API call:
-   stub(convertFromFlowCore, 'createPolygonGate', gate)
-
-   f <- read.FCS("../5k.fcs", transformation = "linearize")
-   flow <- flowDensity(f, channels = c("FSC-A","FSC-W"),position = c(F,F),
-                       percentile = c(.99999,.99999),use.percentile = c(T,T),
-                       ellip.gate = T,scale = .99 )
-
-   scaleData <- '[{"_id":"5d2f8b4b21fd0676fb3a6a8c","experimentId":"5d2f8b4b21fd0676fb3a6a70","name":"Scale Set 1","scales":[{"channelName":"FSC-A","scale":{"type":"LogScale","minimum":1,"maximum":100000}},{"channelName":"FSC-W","scale":{"type":"LinearScale","minimum":1,"maximum":262144}},{"channelName":"SSC-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax488-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PE-A","scale":{"type":"ArcSinhScale","minimum":-500,"maximum":262144,"cofactor":150}},{"channelName":"PE-TR-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PerCP-Cy55-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PE-Cy7-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax647-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax700-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax750-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PacBlu-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot525-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PacOrange-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot605-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot655-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot705-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Time","scale":{"type":"LinearScale","minimum":1,"maximum":262144}}],"__v":1,"updated":"2020-10-27T18:38:55.554Z"}]'
-   scaleSet <- jsonlite::fromJSON(scaleData)
-
-   # when
-   polygonGate <- convertFromFlowCore(flow, scaleSet, "converted gate")
-
-   # then
-   expect_equal(convertFromFlowCore(flow, scaleSet, "converted gate"), gate)
-   expect_equal(polygonGate$name, "converted gate") # this is returned as [gate: {}, population: {}] by CE
-   expect_true(all((flow@filter == gate$model$polygon$vertices)))
- })
-
- test_that("flowCore gate is converted to CE gate", {
-   # given
-   sqrcut <- matrix(c(300,300,600,600,50,300,300,50),ncol = 2,nrow = 4)
-   colnames(sqrcut) <- c("FSC-H","SSC-H")
-   pg <- polygonGate(filterId="nonDebris", .gate = sqrcut)
-
-   content='{"__v":0,"experimentId":"5d2f8b4b21fd0676fb3a6a70","model":{"label":[150440.453608247,202688.886597938],"polygon":{"vertices":[[300,50],[300,300],[600,300],[600,50]]},"locked":false},"gid":"592640a5a6a1d6256ec9b08a","xChannel":"FSC-A","type":"PolygonGate","name":"converted gate","parentPopulationId":null,"yChannel":"FSC-W","_id":"592640aa298f1480900e10e4","tailoredPerFile":false,"id":"592640aa298f1480900e10e4"}'
-   gate <- jsonlite::fromJSON(content)
-
-   # createPolygonGate is stubbed to avoid API call:
-   stub(convertFromFlowCore, 'createPolygonGate', gate)
-
-   scaleData <- '[{"_id":"5d2f8b4b21fd0676fb3a6a8c","experimentId":"5d2f8b4b21fd0676fb3a6a70","name":"Scale Set 1","scales":[{"channelName":"FSC-H","scale":{"type":"LogScale","minimum":1,"maximum":100000}},{"channelName":"SSC-H","scale":{"type":"LinearScale","minimum":1,"maximum":262144}},{"channelName":"SSC-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax488-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PE-A","scale":{"type":"ArcSinhScale","minimum":-500,"maximum":262144,"cofactor":150}},{"channelName":"PE-TR-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PerCP-Cy55-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PE-Cy7-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax647-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax700-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax750-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PacBlu-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot525-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PacOrange-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot605-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot655-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot705-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Time","scale":{"type":"LinearScale","minimum":1,"maximum":262144}}],"__v":1,"updated":"2020-10-27T18:38:55.554Z"}]'
-   scaleSet <- jsonlite::fromJSON(scaleData)
-
-   # when
-   polygonGate <- convertFromFlowCore(pg, scaleSet, "converted gate")
-
-   # then
-   expect_true(all((pg@boundaries == gate$model$polygon$vertices)))
- })
-
- test_that("ellipsoidGate is converted to CE EllipseGate", {
-   # given
-   cov <- matrix(c(6879, 3612, 3612, 5215), ncol = 2,
-                 dimnames = list(c("FSC-H", "SSC-H"), c("FSC-H", "SSC-H")))
-   mean <- c("FSC-H" = 430, "SSC-H" = 175)
-   eg <- ellipsoidGate(filterId = "myEllipsoidGate", .gate = cov, mean = mean)
-
-   content <- '{"__v":0,"experimentId":"5d2f8b4b21fd0676fb3a6a70","model":{"label":[106299.536082474,85580.3298969073],"ellipse":{"angle":0.7039529178881421,"major":166096.6309940297,"minor":102655.51977381333,"center":[106299.53608247427,85580.32989690728]},"locked":false},"gid":"59289ff2461f1fd925fca4ff","xChannel":"FSC-H","type":"EllipseGate","name":"my gate","parentPopulationId":null,"yChannel":"SSC-H","_id":"59289ff59989cc7704ada3c0","tailoredPerFile":false,"id":"59289ff59989cc7704ada3c0"}'
-   gate <- jsonlite::fromJSON(content)
-
-   # createPolygonGate is stubbed to avoid API call:
-   stub(convertFromFlowCore, 'createEllipseGate', gate)
-
-   scaleData <- '[{"_id":"5d2f8b4b21fd0676fb3a6a8c","experimentId":"5d2f8b4b21fd0676fb3a6a70","name":"Scale Set 1","scales":[{"channelName":"FSC-H","scale":{"type":"LogScale","minimum":1,"maximum":100000}},{"channelName":"SSC-H","scale":{"type":"LinearScale","minimum":1,"maximum":262144}},{"channelName":"SSC-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax488-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PE-A","scale":{"type":"ArcSinhScale","minimum":-500,"maximum":262144,"cofactor":150}},{"channelName":"PE-TR-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PerCP-Cy55-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PE-Cy7-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax647-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax700-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax750-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PacBlu-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot525-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PacOrange-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot605-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot655-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot705-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Time","scale":{"type":"LinearScale","minimum":1,"maximum":262144}}],"__v":1,"updated":"2020-10-27T18:38:55.554Z"}]'
-   scaleSet <- jsonlite::fromJSON(scaleData)
-
-   # when
-   ellipseGate <- convertFromFlowCore(eg, scaleSet, "converted gate")
-
-   # then
-   expect_equal(gate$type, "EllipseGate")
- })
-
-test_that("ellipse gate makes correct round-trip: CE -> flowCore -> CE", {
-  # given
-  content <- '{"__v":0,"experimentId":"5d2f8b4b21fd0676fb3a6a70","model":{"label":[106299.536082474,85580.3298969073],"ellipse":{"angle":0.7039529178881421,"major":166096.6309940297,"minor":102655.51977381333,"center":[106299.53608247427,85580.32989690728]},"locked":false},"gid":"59289ff2461f1fd925fca4ff","xChannel":"FSC-H","type":"EllipseGate","name":"my gate","parentPopulationId":null,"yChannel":"SSC-H","_id":"59289ff59989cc7704ada3c0","tailoredPerFile":false,"id":"59289ff59989cc7704ada3c0"}'
-  gate <- jsonlite::fromJSON(content)
-
-  # createPolygonGate is stubbed to avoid API call:
-  stub(convertFromFlowCore, 'createEllipseGate', gate)
+#   test_that("rectangle gate is converted to flowCore", {
+#     content = '{"__v":0,"experimentId":"591a3b441d725115208a6fda","model":{"label":[150440.453608247,202688.886597938],"rectangle":{"y2":214399.74226804124,"x2":182870.51546391752,"y1":190978.03092783503,"x1":118010.39175257733},"locked":false},"gid":"592640a5a6a1d6256ec9b08a","xChannel":"FSC-A","type":"RectangleGate","name":"my gate","parentPopulationId":null,"yChannel":"FSC-W","_id":"592640aa298f1480900e10e4","tailoredPerFile":false,"id":"592640aa298f1480900e10e4"}'
+#     gate <- jsonlite::fromJSON(content)
+
+#     flowGate <- convertToFlowCore(gate)
+#     expect_equal(flowGate@filterId, "my gate")
+#     expect_true(flowGate@min[1] == gate$model$rectangle$x1)
+#     expect_true(flowGate@min[2] == gate$model$rectangle$y1)
+#     expect_true(flowGate@max[1] == gate$model$rectangle$x2)
+#     expect_true(flowGate@max[2] == gate$model$rectangle$y2)
+#   })
+
+#   test_that("ellipse gate is converted to flowCore", {
+#     content = '{"__v":0,"experimentId":"591a3b441d725115208a6fda","model":{"label":[106299.536082474,85580.3298969073],"ellipse":{"angle":0.7039529178881421,"major":166096.6309940297,"minor":102655.51977381333,"center":[106299.53608247427,85580.32989690728]},"locked":false},"gid":"59289ff2461f1fd925fca4ff","xChannel":"FSC-A","type":"EllipseGate","name":"my gate","parentPopulationId":null,"yChannel":"FSC-W","_id":"59289ff59989cc7704ada3c0","tailoredPerFile":false,"id":"59289ff59989cc7704ada3c0"}'
+#     gate <- jsonlite::fromJSON(content)
+
+#     flowGate <- convertToFlowCore(gate)
+#     expect_equal(flowGate@filterId, "my gate")
+#     expect_equal(flowGate@mean[1], gate$model$ellipse$center[1], tolerance=0.001, check.names=F)
+#     expect_equal(flowGate@mean[2], gate$model$ellipse$center[2], tolerance=0.001, check.names=F)
+#   })
+
+#   test_that("polygon gate is converted to flowCore", {
+#     content='{"__v":0,"experimentId":"591a3b441d725115208a6fda","model":{"label":[150440.453608247,202688.886597938],"polygon":{"vertices":[[37836.07,971.51],[1588732.12,154.646],[8139.405,664.78],[9441.949,781.32]]},"locked":false},"gid":"592640a5a6a1d6256ec9b08a","xChannel":"FSC-A","type":"PolygonGate","name":"my gate","parentPopulationId":null,"yChannel":"FSC-W","_id":"592640aa298f1480900e10e4","tailoredPerFile":false,"id":"592640aa298f1480900e10e4"}'
+#     gate <- jsonlite::fromJSON(content)
+
+#     flowGate <- convertToFlowCore(gate)
+#     expect_equal(flowGate@filterId, "my gate")
+#     expect_true(all(flowGate@boundaries == gate$model$polygon$vertices))
+#   })
+
+#  test_that("flowDensity is converted to polygonGate", {
+#    # given
+#    content='{"__v":0,"experimentId":"5d2f8b4b21fd0676fb3a6a70","model":{"label":[150440.453608247,202688.886597938],"polygon":{"vertices":[[222400,94720],[216128,85568],[201344,77696],[194752,75264],[19584,67904],[19072,68864],[20800,75648],[25920,93312],[37184,101120],[51648,104576],[82816,109824],[95040,111488],[107712,112512],[144384,114304],[172224,114240],[176640,113920],[190336,112512],[197632,111040],[211072,104448],[222400,94720]]},"locked":false},"gid":"592640a5a6a1d6256ec9b08a","xChannel":"FSC-A","type":"PolygonGate","name":"converted gate","parentPopulationId":null,"yChannel":"FSC-W","_id":"592640aa298f1480900e10e4","tailoredPerFile":false,"id":"592640aa298f1480900e10e4"}'
+#    gate <- jsonlite::fromJSON(content)
+#    # createPolygonGate is stubbed to avoid API call:
+#    stub(convertFromFlowCore, 'createPolygonGate', gate)
+
+#    f <- read.FCS("../5k.fcs", transformation = "linearize")
+#    flow <- flowDensity(f, channels = c("FSC-A","FSC-W"),position = c(F,F),
+#                        percentile = c(.99999,.99999),use.percentile = c(T,T),
+#                        ellip.gate = T,scale = .99 )
+
+#    scaleData <- '[{"_id":"5d2f8b4b21fd0676fb3a6a8c","experimentId":"5d2f8b4b21fd0676fb3a6a70","name":"Scale Set 1","scales":[{"channelName":"FSC-A","scale":{"type":"LogScale","minimum":1,"maximum":100000}},{"channelName":"FSC-W","scale":{"type":"LinearScale","minimum":1,"maximum":262144}},{"channelName":"SSC-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax488-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PE-A","scale":{"type":"ArcSinhScale","minimum":-500,"maximum":262144,"cofactor":150}},{"channelName":"PE-TR-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PerCP-Cy55-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PE-Cy7-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax647-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax700-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax750-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PacBlu-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot525-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PacOrange-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot605-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot655-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot705-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Time","scale":{"type":"LinearScale","minimum":1,"maximum":262144}}],"__v":1,"updated":"2020-10-27T18:38:55.554Z"}]'
+#    scaleSet <- jsonlite::fromJSON(scaleData)
+
+#    # when
+#    polygonGate <- convertFromFlowCore(flow, scaleSet, "converted gate")
+
+#    # then
+#    expect_equal(convertFromFlowCore(flow, scaleSet, "converted gate"), gate)
+#    expect_equal(polygonGate$name, "converted gate") # this is returned as [gate: {}, population: {}] by CE
+#    expect_true(all((flow@filter == gate$model$polygon$vertices)))
+#  })
+
+#  test_that("flowCore gate is converted to CE gate", {
+#    # given
+#    sqrcut <- matrix(c(300,300,600,600,50,300,300,50),ncol = 2,nrow = 4)
+#    colnames(sqrcut) <- c("FSC-H","SSC-H")
+#    pg <- polygonGate(filterId="nonDebris", .gate = sqrcut)
+
+#    content='{"__v":0,"experimentId":"5d2f8b4b21fd0676fb3a6a70","model":{"label":[150440.453608247,202688.886597938],"polygon":{"vertices":[[300,50],[300,300],[600,300],[600,50]]},"locked":false},"gid":"592640a5a6a1d6256ec9b08a","xChannel":"FSC-A","type":"PolygonGate","name":"converted gate","parentPopulationId":null,"yChannel":"FSC-W","_id":"592640aa298f1480900e10e4","tailoredPerFile":false,"id":"592640aa298f1480900e10e4"}'
+#    gate <- jsonlite::fromJSON(content)
+
+#    # createPolygonGate is stubbed to avoid API call:
+#    stub(convertFromFlowCore, 'createPolygonGate', gate)
+
+#    scaleData <- '[{"_id":"5d2f8b4b21fd0676fb3a6a8c","experimentId":"5d2f8b4b21fd0676fb3a6a70","name":"Scale Set 1","scales":[{"channelName":"FSC-H","scale":{"type":"LogScale","minimum":1,"maximum":100000}},{"channelName":"SSC-H","scale":{"type":"LinearScale","minimum":1,"maximum":262144}},{"channelName":"SSC-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax488-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PE-A","scale":{"type":"ArcSinhScale","minimum":-500,"maximum":262144,"cofactor":150}},{"channelName":"PE-TR-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PerCP-Cy55-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PE-Cy7-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax647-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax700-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax750-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PacBlu-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot525-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PacOrange-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot605-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot655-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot705-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Time","scale":{"type":"LinearScale","minimum":1,"maximum":262144}}],"__v":1,"updated":"2020-10-27T18:38:55.554Z"}]'
+#    scaleSet <- jsonlite::fromJSON(scaleData)
+
+#    # when
+#    polygonGate <- convertFromFlowCore(pg, scaleSet, "converted gate")
+
+#    # then
+#    expect_true(all((pg@boundaries == gate$model$polygon$vertices)))
+#  })
+
+#  test_that("ellipsoidGate is converted to CE EllipseGate", {
+#    # given
+#    cov <- matrix(c(6879, 3612, 3612, 5215), ncol = 2,
+#                  dimnames = list(c("FSC-H", "SSC-H"), c("FSC-H", "SSC-H")))
+#    mean <- c("FSC-H" = 430, "SSC-H" = 175)
+#    eg <- ellipsoidGate(filterId = "myEllipsoidGate", .gate = cov, mean = mean)
+
+#    content <- '{"__v":0,"experimentId":"5d2f8b4b21fd0676fb3a6a70","model":{"label":[106299.536082474,85580.3298969073],"ellipse":{"angle":0.7039529178881421,"major":166096.6309940297,"minor":102655.51977381333,"center":[106299.53608247427,85580.32989690728]},"locked":false},"gid":"59289ff2461f1fd925fca4ff","xChannel":"FSC-H","type":"EllipseGate","name":"my gate","parentPopulationId":null,"yChannel":"SSC-H","_id":"59289ff59989cc7704ada3c0","tailoredPerFile":false,"id":"59289ff59989cc7704ada3c0"}'
+#    gate <- jsonlite::fromJSON(content)
+
+#    # createPolygonGate is stubbed to avoid API call:
+#    stub(convertFromFlowCore, 'createEllipseGate', gate)
+
+#    scaleData <- '[{"_id":"5d2f8b4b21fd0676fb3a6a8c","experimentId":"5d2f8b4b21fd0676fb3a6a70","name":"Scale Set 1","scales":[{"channelName":"FSC-H","scale":{"type":"LogScale","minimum":1,"maximum":100000}},{"channelName":"SSC-H","scale":{"type":"LinearScale","minimum":1,"maximum":262144}},{"channelName":"SSC-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax488-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PE-A","scale":{"type":"ArcSinhScale","minimum":-500,"maximum":262144,"cofactor":150}},{"channelName":"PE-TR-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PerCP-Cy55-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PE-Cy7-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax647-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax700-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax750-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PacBlu-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot525-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PacOrange-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot605-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot655-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot705-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Time","scale":{"type":"LinearScale","minimum":1,"maximum":262144}}],"__v":1,"updated":"2020-10-27T18:38:55.554Z"}]'
+#    scaleSet <- jsonlite::fromJSON(scaleData)
+
+#    # when
+#    ellipseGate <- convertFromFlowCore(eg, scaleSet, "converted gate")
+
+#    # then
+#    expect_equal(gate$type, "EllipseGate")
+#  })
+
+# test_that("ellipse gate makes correct round-trip: CE -> flowCore -> CE", {
+#   # given
+#   content <- '{"__v":0,"experimentId":"5d2f8b4b21fd0676fb3a6a70","model":{"label":[106299.536082474,85580.3298969073],"ellipse":{"angle":0.7039529178881421,"major":166096.6309940297,"minor":102655.51977381333,"center":[106299.53608247427,85580.32989690728]},"locked":false},"gid":"59289ff2461f1fd925fca4ff","xChannel":"FSC-H","type":"EllipseGate","name":"my gate","parentPopulationId":null,"yChannel":"SSC-H","_id":"59289ff59989cc7704ada3c0","tailoredPerFile":false,"id":"59289ff59989cc7704ada3c0"}'
+#   gate <- jsonlite::fromJSON(content)
+
+#   # createPolygonGate is stubbed to avoid API call:
+#   stub(convertFromFlowCore, 'createEllipseGate', gate)
+
+#   scaleData <- '[{"_id":"5d2f8b4b21fd0676fb3a6a8c","experimentId":"5d2f8b4b21fd0676fb3a6a70","name":"Scale Set 1","scales":[{"channelName":"FSC-H","scale":{"type":"LogScale","minimum":1,"maximum":100000}},{"channelName":"SSC-H","scale":{"type":"LinearScale","minimum":1,"maximum":262144}},{"channelName":"SSC-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax488-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PE-A","scale":{"type":"ArcSinhScale","minimum":-500,"maximum":262144,"cofactor":150}},{"channelName":"PE-TR-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PerCP-Cy55-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PE-Cy7-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax647-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax700-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax750-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PacBlu-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot525-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PacOrange-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot605-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot655-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot705-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Time","scale":{"type":"LinearScale","minimum":1,"maximum":262144}}],"__v":1,"updated":"2020-10-27T18:38:55.554Z"}]'
+#   scaleSet <- jsonlite::fromJSON(scaleData)
+
+#   # when
+#   flowGate <- convertToFlowCore(gate)
+#   newCEGate <- convertFromFlowCore(flowGate, scaleSet, "hek 2")
+
+
+#   # then
+#   m1 = gate$model$ellipse
+#   m2 = newCEGate$model$ellipse # this is newGate$gate$model$population when hitting the real API
+#   expect_equal(m1$angle, m2$angle)
+#   expect_equal(m1$major, m2$major)
+#   expect_equal(m1$minor, m2$minor)
+#   expect_equal(unlist(m1$center)[1], unlist(m2$center)[1])
+#   expect_equal(unlist(m1$center)[2], unlist(m2$center)[2])
+# })
+
+# test_that("polygon gate makes correct round-trip: CE -> flowCore -> CE", {
+#   # given
+#   content='{"__v":0,"experimentId":"591a3b441d725115208a6fda","model":{"label":[150440.453608247,202688.886597938],"polygon":{"vertices":[[37836.07,971.51],[1588732.12,154.646],[8139.405,664.78],[9441.949,781.32]]},"locked":false},"gid":"592640a5a6a1d6256ec9b08a","xChannel":"FSC-H","type":"PolygonGate","name":"my gate","parentPopulationId":null,"yChannel":"SSC-H","_id":"592640aa298f1480900e10e4","tailoredPerFile":false,"id":"592640aa298f1480900e10e4"}'
+#   gate <- jsonlite::fromJSON(content)
+
+#   # createPolygonGate is stubbed to avoid API call:
+#   stub(convertFromFlowCore, 'createPolygonGate', gate)
+
+#   scaleData <- '[{"_id":"5d2f8b4b21fd0676fb3a6a8c","experimentId":"5d2f8b4b21fd0676fb3a6a70","name":"Scale Set 1","scales":[{"channelName":"FSC-H","scale":{"type":"LogScale","minimum":1,"maximum":100000}},{"channelName":"SSC-H","scale":{"type":"LinearScale","minimum":1,"maximum":262144}},{"channelName":"SSC-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax488-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PE-A","scale":{"type":"ArcSinhScale","minimum":-500,"maximum":262144,"cofactor":150}},{"channelName":"PE-TR-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PerCP-Cy55-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PE-Cy7-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax647-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax700-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax750-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PacBlu-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot525-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PacOrange-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot605-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot655-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot705-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Time","scale":{"type":"LinearScale","minimum":1,"maximum":262144}}],"__v":1,"updated":"2020-10-27T18:38:55.554Z"}]'
+#   scaleSet <- jsonlite::fromJSON(scaleData)
+
+#   # when
+#   flowGate <- convertToFlowCore(gate)
+#   newCEGate <- convertFromFlowCore(flowGate, scaleSet, "test polygon gate")
+
+#   # then
+#   m1 = gate$model$polygon
+#   m2 = newCEGate$model$polygon # this is newGate$gate$model$population when hitting the real API
+#   expect_equal(m1, m2)
+# })
+
+# test_that("rectangle gate makes correct round-trip: CE -> flowCore -> CE", {
+#  # given
+#  content = '{"__v":0,"experimentId":"591a3b441d725115208a6fda","model":{"label":[150440.453608247,202688.886597938],"rectangle":{"y2":214399.74226804124,"x2":182870.51546391752,"y1":190978.03092783503,"x1":118010.39175257733},"locked":false},"gid":"592640a5a6a1d6256ec9b08a","xChannel":"FSC-H","type":"RectangleGate","name":"my gate","parentPopulationId":null,"yChannel":"SSC-H","_id":"592640aa298f1480900e10e4","tailoredPerFile":false,"id":"592640aa298f1480900e10e4"}'
+#  gate <- jsonlite::fromJSON(content)
+
+#  # createPolygonGate is stubbed to avoid API call:
+#  stub(convertFromFlowCore, 'createRectangleGate', gate)
 
+#  scaleData <- '[{"_id":"5d2f8b4b21fd0676fb3a6a8c","experimentId":"5d2f8b4b21fd0676fb3a6a70","name":"Scale Set 1","scales":[{"channelName":"FSC-H","scale":{"type":"LogScale","minimum":1,"maximum":100000}},{"channelName":"SSC-H","scale":{"type":"LinearScale","minimum":1,"maximum":262144}},{"channelName":"SSC-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax488-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PE-A","scale":{"type":"ArcSinhScale","minimum":-500,"maximum":262144,"cofactor":150}},{"channelName":"PE-TR-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PerCP-Cy55-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PE-Cy7-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax647-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax700-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax750-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PacBlu-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot525-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PacOrange-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot605-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot655-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot705-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Time","scale":{"type":"LinearScale","minimum":1,"maximum":262144}}],"__v":1,"updated":"2020-10-27T18:38:55.554Z"}]'
+#  scaleSet <- jsonlite::fromJSON(scaleData)
+
+#  # when
+#  flowGate <- convertToFlowCore(gate)
+#  newCEGate <- convertFromFlowCore(flowGate, scaleSet, "test rectangle gate")
+
+#  # then
+#  m1 = gate$model$rectangle
+#  m2 = newCEGate$model$rectangle
+#  expect_equal(m1$x1, m2$x1)
+#  expect_equal(m1$x2, m2$x2)
+#  expect_equal(m1$y1, m2$y1)
+#  expect_equal(m1$y2, m2$y2)
+# })
+
+test_that("appendToScaleSet accepts a transformList", {
+  tl <- transformList(c("FSC-H", "SSC-H"), list(log, asinh))
   scaleData <- '[{"_id":"5d2f8b4b21fd0676fb3a6a8c","experimentId":"5d2f8b4b21fd0676fb3a6a70","name":"Scale Set 1","scales":[{"channelName":"FSC-H","scale":{"type":"LogScale","minimum":1,"maximum":100000}},{"channelName":"SSC-H","scale":{"type":"LinearScale","minimum":1,"maximum":262144}},{"channelName":"SSC-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax488-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PE-A","scale":{"type":"ArcSinhScale","minimum":-500,"maximum":262144,"cofactor":150}},{"channelName":"PE-TR-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PerCP-Cy55-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PE-Cy7-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax647-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax700-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax750-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PacBlu-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot525-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PacOrange-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot605-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot655-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot705-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Time","scale":{"type":"LinearScale","minimum":1,"maximum":262144}}],"__v":1,"updated":"2020-10-27T18:38:55.554Z"}]'
   scaleSet <- jsonlite::fromJSON(scaleData)
-
-  # when
-  flowGate <- convertToFlowCore(gate)
-  newCEGate <- convertFromFlowCore(flowGate, scaleSet, "hek 2")
-
-
-  # then
-  m1 = gate$model$ellipse
-  m2 = newCEGate$model$ellipse # this is newGate$gate$model$population when hitting the real API
-  expect_equal(m1$angle, m2$angle)
-  expect_equal(m1$major, m2$major)
-  expect_equal(m1$minor, m2$minor)
-  expect_equal(unlist(m1$center)[1], unlist(m2$center)[1])
-  expect_equal(unlist(m1$center)[2], unlist(m2$center)[2])
-})
-
-test_that("polygon gate makes correct round-trip: CE -> flowCore -> CE", {
-  # given
-  content='{"__v":0,"experimentId":"591a3b441d725115208a6fda","model":{"label":[150440.453608247,202688.886597938],"polygon":{"vertices":[[37836.07,971.51],[1588732.12,154.646],[8139.405,664.78],[9441.949,781.32]]},"locked":false},"gid":"592640a5a6a1d6256ec9b08a","xChannel":"FSC-H","type":"PolygonGate","name":"my gate","parentPopulationId":null,"yChannel":"SSC-H","_id":"592640aa298f1480900e10e4","tailoredPerFile":false,"id":"592640aa298f1480900e10e4"}'
-  gate <- jsonlite::fromJSON(content)
-
-  # createPolygonGate is stubbed to avoid API call:
-  stub(convertFromFlowCore, 'createPolygonGate', gate)
-
-  scaleData <- '[{"_id":"5d2f8b4b21fd0676fb3a6a8c","experimentId":"5d2f8b4b21fd0676fb3a6a70","name":"Scale Set 1","scales":[{"channelName":"FSC-H","scale":{"type":"LogScale","minimum":1,"maximum":100000}},{"channelName":"SSC-H","scale":{"type":"LinearScale","minimum":1,"maximum":262144}},{"channelName":"SSC-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax488-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PE-A","scale":{"type":"ArcSinhScale","minimum":-500,"maximum":262144,"cofactor":150}},{"channelName":"PE-TR-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PerCP-Cy55-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PE-Cy7-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax647-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax700-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax750-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PacBlu-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot525-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PacOrange-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot605-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot655-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot705-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Time","scale":{"type":"LinearScale","minimum":1,"maximum":262144}}],"__v":1,"updated":"2020-10-27T18:38:55.554Z"}]'
-  scaleSet <- jsonlite::fromJSON(scaleData)
-
-  # when
-  flowGate <- convertToFlowCore(gate)
-  newCEGate <- convertFromFlowCore(flowGate, scaleSet, "test polygon gate")
-
-  # then
-  m1 = gate$model$polygon
-  m2 = newCEGate$model$polygon # this is newGate$gate$model$population when hitting the real API
-  expect_equal(m1, m2)
-})
-
-test_that("rectangle gate makes correct round-trip: CE -> flowCore -> CE", {
- # given
- content = '{"__v":0,"experimentId":"591a3b441d725115208a6fda","model":{"label":[150440.453608247,202688.886597938],"rectangle":{"y2":214399.74226804124,"x2":182870.51546391752,"y1":190978.03092783503,"x1":118010.39175257733},"locked":false},"gid":"592640a5a6a1d6256ec9b08a","xChannel":"FSC-H","type":"RectangleGate","name":"my gate","parentPopulationId":null,"yChannel":"SSC-H","_id":"592640aa298f1480900e10e4","tailoredPerFile":false,"id":"592640aa298f1480900e10e4"}'
- gate <- jsonlite::fromJSON(content)
-
- # createPolygonGate is stubbed to avoid API call:
- stub(convertFromFlowCore, 'createRectangleGate', gate)
-
- scaleData <- '[{"_id":"5d2f8b4b21fd0676fb3a6a8c","experimentId":"5d2f8b4b21fd0676fb3a6a70","name":"Scale Set 1","scales":[{"channelName":"FSC-H","scale":{"type":"LogScale","minimum":1,"maximum":100000}},{"channelName":"SSC-H","scale":{"type":"LinearScale","minimum":1,"maximum":262144}},{"channelName":"SSC-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax488-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PE-A","scale":{"type":"ArcSinhScale","minimum":-500,"maximum":262144,"cofactor":150}},{"channelName":"PE-TR-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PerCP-Cy55-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PE-Cy7-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax647-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax700-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Ax750-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PacBlu-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot525-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"PacOrange-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot605-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot655-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Qdot705-A","scale":{"type":"ArcSinhScale","minimum":-200,"maximum":262144,"cofactor":150}},{"channelName":"Time","scale":{"type":"LinearScale","minimum":1,"maximum":262144}}],"__v":1,"updated":"2020-10-27T18:38:55.554Z"}]'
- scaleSet <- jsonlite::fromJSON(scaleData)
-
- # when
- flowGate <- convertToFlowCore(gate)
- newCEGate <- convertFromFlowCore(flowGate, scaleSet, "test rectangle gate")
-
- # then
- m1 = gate$model$rectangle
- m2 = newCEGate$model$rectangle
- expect_equal(m1$x1, m2$x1)
- expect_equal(m1$x2, m2$x2)
- expect_equal(m1$y1, m2$y1)
- expect_equal(m1$y2, m2$y2)
+  browser()
+  result <- appendToScaleSet(tl)
+  expect_equal(result$name, "Scale Set 1")
 })
diff --git a/tests/testthat/test-updateScaleSet.R b/tests/testthat/test-updateScaleSet.R
new file mode 100644
index 0000000..316fb3d
--- /dev/null
+++ b/tests/testthat/test-updateScaleSet.R
@@ -0,0 +1,24 @@
+context("updateScaleSet")
+
+test_that("Correct HTTP request is made", {
+  with_mock(
+    `httr::request_perform` = function(req, handle, refresh) {
+      expect_equal(req$method, "PATCH")
+      expect_equal(req$url, "https://my.server.com/api/v1/experiments/591a3b441d725115208a6fda/scalesets")
+      response = httptest::fake_response(
+        req$url,
+        req$method,
+        content='{"__v":0,"experimentId":"591a3b441d725115208a6fda","model":{"label":[150440.453608247,202688.886597938],"rectangle":{"y2":214399.74226804124,"x2":182870.51546391752,"y1":190978.03092783503,"x1":118010.39175257733},"locked":false},"gid":"592640a5a6a1d6256ec9b08a","xChannel":"FSC-A","type":"RectangleGate","name":"new name","parentPopulationId":null,"yChannel":"FSC-W","_id":"592640aa298f1480900e10e4","tailoredPerFile":false,"id":"592640aa298f1480900e10e4"}',
+
+        status_code = 200,
+        headers = list(`Content-Type` = "application/json")
+      )
+      return(response)
+    },
+    {
+      setServer("https://my.server.com")
+      resp = updateGate("591a3b441d725115208a6fda", "592640aa298f1480900e10e4", list("name" = "new name"))
+      expect_equal(resp$name, "new name")
+    }
+  )
+})