library(flowWorkspace)
fcsdir <- "/loc/no-backup/mike/JJ/"
wsfile <- list.files(fcsdir,pattern="*.xml", full =T)
ws <- openWorkspace(wsfile)
ws
## FlowJo Workspace Version 2.0
## File location: /loc/no-backup/mike/JJ
## File name: JJ_FlowJo_.xml
## Workspace is open.
##
## Groups in Workspace
## Name Num.Samples
## 1 All Samples 47
## 2 CompensationPanel2 12
## 3 FMO Panel 2 11
## 4 Test 6
## 5 FMO Compensation Panel2 13
You want to AVOID the first group ‘All Samples’
suppressMessages(gs <- parseWorkspace(ws, name = "FMO Panel 2"))#here select the third group instead
## mac version of flowJo workspace recognized.
## Warning in .parseWorkspace(xmlFileName = file.path(obj@path, obj@file), :
## Due to the different gating tree structures, a list of GatingSets is
## returned instead!
Be aware of the warning message
gs
## [[1]]
## A GatingSet with 1 samples
##
## [[2]]
## A GatingSet with 1 samples
##
## [[3]]
## A GatingSet with 1 samples
##
## [[4]]
## A GatingSet with 1 samples
##
## [[5]]
## A GatingSet with 1 samples
##
## [[6]]
## A GatingSet with 1 samples
##
## [[7]]
## A GatingSet with 1 samples
##
## [[8]]
## A GatingSet with 1 samples
##
## [[9]]
## A GatingSet with 1 samples
##
## [[10]]
## A GatingSet with 1 samples
##
## [[11]]
## A GatingSet with 1 samples
Examine the difference by checking the nodes
getNodes(gs[[1]], path = "auto")
## [1] "root" "Cells" "SSC-Singlets" "FSC-Singlets"
## [5] "FL1xFL2" "FL3xFL4" "FL5xFL6" "FL7xFL8"
## [9] "FL9xFL10" "FL11xFL12" "CD10pos"
getNodes(gs[[2]], path = "auto")
## [1] "root" "Cells" "SSC-Singlets" "FSC-Singlets"
## [5] "FL1xFL2" "FL3xFL4" "FL5xFL6" "FL7xFL8"
## [9] "FL9xFL10" "FL11xFL12" "CD150"
getNodes(gs[[3]], path = "auto")
## [1] "root" "Cells" "SSC-Singlets" "FSC-Singlets"
## [5] "FL1xFL2" "FL3xFL4" "FL5xFL6" "FL7xFL8"
## [9] "FL9xFL10" "FL11xFL12" "CD19pos"
They seem to differ by the last node
plot the tree and gates
gh <- gs[[1]][[1]]
plot(gh)
plotGate(gh)
compare the stats
getPopStats(gh)
## flowCore.freq flowJo.freq flowJo.count flowCore.count node
## 1: 1.000000000 1.0000000 33742 33742 root
## 2: 0.985655859 0.9864264 33284 33258 Cells
## 3: 0.727343797 0.7046629 23454 24190 SSC-Singlets
## 4: 0.477842084 0.4920696 11541 11559 FSC-Singlets
## 5: 1.000000000 0.0000000 0 11559 FL1xFL2
## 6: 0.998788823 0.0000000 0 11545 FL3xFL4
## 7: 1.000000000 0.0000000 0 11559 FL5xFL6
## 8: 0.999826975 0.0000000 0 11557 FL7xFL8
## 9: 0.999740462 0.0000000 0 11556 FL9xFL10
## 10: 1.000000000 0.0000000 0 11559 FL11xFL12
## 11: 0.003027944 0.0000000 0 35 CD10pos