Comments (4)
jspidlen
commented on July 29, 2024
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
…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)
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gfinak
commented on July 29, 2024
Thanks, Josef, that's very helpful.
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mikejiang
commented on July 29, 2024
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_2output 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
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jspidlen
commented on July 29, 2024
Great, thanks Mike, glad it has worked!
Josef
…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>
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Related Issues (20)
- CytoML Xml File Parsing Issues HOT 8
- Issue Parsing FlowJo (v10.7.2) XML File HOT 3
- FCS Express compatibility HOT 7
- Get indices of gated events from a FJ workspace / alternative to flowjo_to_gatingset HOT 5
- gs-to-flowjo Singularity issue HOT 2
- Ellipses coordinates are not correct in Gating Set after flowJo workspace parsing - v2.9.0 HOT 4
- R Session Aborts when calling flowjo_to_gatingset() more than once HOT 3
- gatingset_to_flowjo() fails with unsupported transformation: LIN
- Using FlowJo gating on pre-compensated, pre-transformed FCS files HOT 5
- flowjo_to_gatingset troubleshoot: "unknown tranformation type!transforms:linear" HOT 3
- flowjo_to_gatingset(), colname not found: error HOT 2
- Export populations as dataframe from a FlowJo workspace HOT 2
- extract inverse transform
- flowjo_to_gatingset does not accept data.frame as path HOT 5
- flowCore::read.FCS works but CytoML::flowjo_to_gatingset fails; no valid FCS file HOT 11
- boolean gate error
- Incompatible with Apple Silicon Mac HOT 7
- flowjo_to_gatingset ignore range as defined in FCS files HOT 3
- Support for FCS 3.2? HOT 4
- gatingset_to_flowjo hangs
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