support exporting clustering results to flowJo

[mikejiang]

@jspidlen, Does flowJo xml have a general way to annotate the bool or integer event indices representing the cell memberships produced by the clustering algorithm? We'd like to run some in-house clustering method and store the cluster membership or labels in GatingSet and then export to flowJo.
I know flowJo supports several specific plugins. Are these population nodes generated by these plugins only meaningful for the existing plugins?(Thus not suitable for storing results from other clustering methods)

[jspidlen]

Hi Mike, This information isn't stored in the XML or the plugin nodes. It's typically based on a derived parameter (such as some sort of a cluster id) that lives in a separate file, which is merged-in with the corresponding data file, and then gates are placed on the cluster id parameter to define populations. The XML workspace (.wsp) file will describe what derived parameters should be merged in with what FCS samples, and how the populations are defined on those. For you, the easiest may be to reverse-engineer the details from a plugin that does that. For example, 1) Save a simple workspace. 2) Take for example the PhenoGraph plugin and run it on a population. 3) Delete the PhenoGraph node once the run has completed successfully. (You don't need it, you only need the resulting phenograph cluster id derived parameter and the gates placed around distinct values of that parameter) 4) Save the workspace as a new version. 5) Compare the workspaces saved in step 1 and 5, this should tell you how to modify a workspace to specify that a CSV file with derived parameters should be merged in as well as how to place gates on that derived parameter to define populations. Also, look at the CSV file to figure out the details of how to store the values of the derived parameter/cluster ids. Hope that helps. Best, Josef

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On Thu, Aug 23, 2018, 1:44 PM Mike Jiang ***@***.***> wrote: @jspidlen <https://github.com/jspidlen>, Does flowJo xml have a general way to annotate the bool or integer event indices representing the cell memberships produced by the clustering algorithm? We'd like to run some in-house clustering method and store the cluster membership or labels in GatingSet and then export to flowJo. I know flowJo supports several specific plugins. Are these population nodes generated by these plugins only meaningful for the existing plugins?(Thus not suitable for storing results from other clustering methods) — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#45>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAaU2v0PHg4g2S3Ykqxb0FB1YjsyLo34ks5uTxRIgaJpZM4WKUbC> .

[gfinak]

Thanks, Josef, that's very helpful.

[mikejiang]

Here is the preliminary results:

load the gatingset

library(flowWorkspace)
liibrary(CytoML)
 dataDir <- system.file("extdata",package="flowWorkspaceData")
  gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE))
  gh <- gs[[1]]
  params <- parameters(getGate(gh, "CD4"))
  Rm("CD4", gs)
  Rm("CD8", gs)

run flowClust on cd3 parent

  fr <- getData(gh, "CD3+")
  library(flowClust)
  res <- flowClust(fr, varNames = params, K = 2, nu = 1, trans = 0)
  plot(res, data = fr)

add clustering results as a factor vector

 res <- Map(res)
  res <- as.factor(res)
  add(gh, res, parent = "CD3+", name = "flowclust")
plot(gs, "CD3+")

getPopStats(gs[[1]])[5:6,c(1,3,5)]
   openCyto.freq openCyto.count        node
1:     0.2998366          16336 flowclust_1
2:     0.6687407          36435 flowclust_2

output to flowJo

outFile <- "~/test.wsp"
GatingSet2flowJo(gs, outFile)
> DerivedParameter: /home/wjiang2/CytoTrol_CytoTrol_1.fcs.flowclust.CD3+.EPA.csv
[1] "~/test.wsp"

load ws in flowJo

new parameter

display cluster node flowclust_1

display it in different dimensions

[jspidlen]

Great, thanks Mike, glad it has worked! Josef

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On Tue, Aug 28, 2018 at 2:01 PM Mike Jiang ***@***.***> wrote: Here is the preliminary results: load the gatingset library(flowWorkspace) liibrary(CytoML) dataDir <- system.file("extdata",package="flowWorkspaceData") gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE)) gh <- gs[[1]] params <- parameters(getGate(gh, "CD4")) Rm("CD4", gs) Rm("CD8", gs) run flowClust on cd3 parent fr <- getData(gh, "CD3+") library(flowClust) res <- flowClust(fr, varNames = params, K = 2, nu = 1, trans = 0) plot(res, data = fr) [image: image] <https://user-images.githubusercontent.com/1385649/44749660-0d698380-aac8-11e8-8eb0-74afc9dab8b4.png> add clustering results as a factor vector res <- Map(res) res <- as.factor(res) add(gh, res, parent = "CD3+", name = "flowclust") plot(gs, "CD3+") [image: image] <https://user-images.githubusercontent.com/1385649/44749843-9a144180-aac8-11e8-809e-bbdd21702a5b.png> getPopStats(gs[[1]])[5:6,c(1,3,5)] openCyto.freq openCyto.count node1: 0.2998366 16336 flowclust_12: 0.6687407 36435 flowclust_2 output to flowJo outFile <- "~/test.wsp" GatingSet2flowJo(gs, outFile)> DerivedParameter: /home/wjiang2/CytoTrol_CytoTrol_1.fcs.flowclust.CD3+.EPA.csv [1] "~/test.wsp" load ws in flowJo [image: image] <https://user-images.githubusercontent.com/1385649/44750623-b4e7b580-aaca-11e8-98c2-0ce52f1558e6.png> new parameter [image: image] <https://user-images.githubusercontent.com/1385649/44750699-e9f40800-aaca-11e8-8343-9fc0fb9d2ad5.png> — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#45 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAaU2pc5bdEJXdbU_CfjhvHLoQlLbu_rks5uVa_GgaJpZM4WKUbC> .