Issues with CytoML vignette #163
Description
My ultimate goal is to create a cytoML file from a CytoExploreR gating set that I can read in with the python flowkit package.
As a starting place I wanted to read in well constructed code from the cytoML vignette but encountered several issues worth providing (potential bug/issue status) feedback on the CytoML vignette. The files created by the vignette code are attached.
A summary of the isssues encountered:
- all the references in the schema files produce 404 errors from the ISAC site
- Running the vignette suggests that it contains multiple depricated commands: gating(), toggle.helperGates()
- The use of gatingset_to_cytobank(gs, outFile) produces over 50 errors of the form:
Warning messages:
1: In gatingset_to_cytobank(gs, outFile) :
With 'cytobank.default.scale' set to 'TRUE', data and gates will be re-transformed with cytobank's default scaling settings, which may affect how gates look like.
2: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gating
3: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gating
...
48: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
49: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
50: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gating
- The use of gatingset_to_flowjo(gs, outFile) produces a cryptic message "INFO: Could not find files for the given pattern(s)." before ultimately returning TRUE from the docker image.
Here is the console output from running the code:
> library(ncdfFlow)
Loading required package: flowCore
Loading required package: BH
> library(flowWorkspace)
As part of improvements to flowWorkspace, some behavior of
GatingSet objects has changed. For details, please read the section
titled "The cytoframe and cytoset classes" in the package vignette:
vignette("flowWorkspace-Introduction", "flowWorkspace")
> library(CytoML)
> dataDir <- system.file("extdata",package="flowWorkspaceData")
> #load raw FCS
> fs <- load_cytoset_from_fcs(file.path(dataDir,"CytoTrol_CytoTrol_1.fcs"))
> gs <- GatingSet(fs)
>
> #compensate
> comp <- spillover(fs[[1]])[["SPILL"]]
> chnls <- colnames(comp)
> comp <- compensation(comp)
> gs <- compensate(gs, comp)
>
> #transform
> trans <- flowjo_biexp_trans()
> trans <- transformerList(chnls, trans)
> gs <- transform(gs, trans)
>
> library(openCyto)
> #load the original template for tcell panel
> tbl <- data.table::fread(system.file("extdata/gating_template/tcell.csv", package = "openCyto"))
> #modify some paramters to fit the current data range
> tbl[5, gating_args:= "gate_range = c(1e3, 3e3)"]
> tbl[c(8,11), gating_args:= "gate_range = c(2e3, 3e3)"]
> #write the new template to disc
> gtFile <- tempfile()
> write.csv(tbl, file = gtFile)
> ##reload the new template
> gt <- gatingTemplate(gtFile)
expanding pop: -/++/-
expanding pop: +/-+/-
expanding pop: +/-+/-
Adding population:nonDebris
Adding population:singlets
Adding population:lymph
Adding population:cd3
Adding population:cd4+
Adding population:cd8+
Adding population:cd4+cd8+
Adding population:cd4-cd8+
Adding population:cd4+cd8-
Adding population:cd4-cd8-
Adding population:CD38+
Adding population:HLA+
Adding population:activated cd4
Adding population:CD38+
Adding population:HLA+
Adding population:activated cd8
Adding population:CD45_neg
Adding population:CCR7_gate
Adding population:CCR7+CD45RA+
Adding population:CCR7-CD45RA+
Adding population:CCR7+CD45RA-
Adding population:CCR7-CD45RA-
Adding population:CCR7+
Adding population:CD45RA+
Adding population:CCR7+CD45RA+
Adding population:CCR7-CD45RA+
Adding population:CCR7+CD45RA-
Adding population:CCR7-CD45RA-
> #run the gating
> gating(gt, gs)
Gating for 'nonDebris'
done!
done.
Gating for 'singlets'
done!
done.
Preprocessing for 'lymph'
'K' argument is missing in prior_flowclust! Using default setting: K = 2.
You should set this to the same value as 'K' in the call to flowClust.
Gating for 'lymph'
Using the serial version of flowClust
done!
done.
Gating for 'cd3'
done!
done.
Gating for 'cd8+'
done!
done.
Gating for 'cd4+'
done!
done.
Population 'cd4-cd8-'
done.
Population 'cd4+cd8-'
done.
Gating for 'CD45_neg'
done!
done.
Gating for 'CCR7_gate'
The prior specification has no effect when usePrior=no
Using the serial version of flowClust
done!
done.
Population 'CCR7-CD45RA-'
done!
done.
Population 'CCR7+CD45RA-'
done!
done.
Population 'CCR7-CD45RA+'
done!
done.
Population 'CCR7+CD45RA+'
done!
done.
Preprocessing for 'HLA+'
Gating for 'HLA+'
done!
done.
Preprocessing for 'CD38+'
Gating for 'CD38+'
done!
done.
Population 'activated cd4'
done.
Population 'cd4-cd8+'
done.
Gating for 'CD45RA+'
done!
done.
Gating for 'CCR7+'
done!
done.
Population 'CCR7-CD45RA-'
done.
Population 'CCR7+CD45RA-'
done.
Population 'CCR7-CD45RA+'
done.
Population 'CCR7+CD45RA+'
done.
Preprocessing for 'HLA+'
Gating for 'HLA+'
done!
done.
Preprocessing for 'CD38+'
Gating for 'CD38+'
done!
done.
Population 'activated cd8'
done.
Population 'cd4+cd8+'
done.
finished.
Warning messages:
1: In gating(gt, gs) : 'gating' is deprecated.
Use 'gt_gating' instead.
See help("Deprecated")
2: In getChannelMarker(parent_data[[1, use.exprs = FALSE]], channel) :
HLA is partially matched with V545-AHLA-DR V500
3: In getChannelMarker(frm, channel) :
HLA is partially matched with V545-AHLA-DR V500
4: In getChannelMarker(fr, dim) :
HLA is partially matched with V545-AHLA-DR V500
5: In getChannelMarker(parent_data[[1, use.exprs = FALSE]], channel) :
HLA is partially matched with V545-AHLA-DR V500
6: In getChannelMarker(frm, channel) :
HLA is partially matched with V545-AHLA-DR V500
7: In getChannelMarker(fr, dim) :
HLA is partially matched with V545-AHLA-DR V500
> #hide the gates that are not of interest
> toggle.helperGates(gt, gs)
Warning message:
In toggle.helperGates(gt, gs) : 'toggle.helperGates' is deprecated.
Use 'gt_toggle_helpergates' instead.
See help("Deprecated")
> #visualize the gates
> library(ggcyto)
Loading required package: ggplot2
> autoplot(gs[[1]])
Coordinate system already present. Adding new coordinate system, which will replace the
existing one.
Coordinate system already present. Adding new coordinate system, which will replace the
existing one.
Coordinate system already present. Adding new coordinate system, which will replace the
existing one.
Coordinate system already present. Adding new coordinate system, which will replace the
existing one.
Coordinate system already present. Adding new coordinate system, which will replace the
existing one.
Coordinate system already present. Adding new coordinate system, which will replace the
existing one.
Coordinate system already present. Adding new coordinate system, which will replace the
existing one.
Coordinate system already present. Adding new coordinate system, which will replace the
existing one.
Coordinate system already present. Adding new coordinate system, which will replace the
existing one.
>
> outFile <- "cytoML_CB_Ref.xml"
> gatingset_to_cytobank(gs, outFile)
[1] "cytoML_CB_Ref.xml"
There were 50 or more warnings (use warnings() to see the first 50)
>
> outFile <- "cytoML_FJ_Ref.wsp"
> gatingset_to_flowjo(gs, outFile)
INFO: Could not find files for the given pattern(s).
Using docker image public.ecr.aws/x4k5d9i7/cytoverse/gs-to-wsp:latest to write FlowJo workspace...
[1] TRUE
Windows 11, R 4.5.0, latest bioconductor, ozette cytoverse, docker
R version 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six"
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Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
[Workspace loaded from D:/VSCode_Projects/Flowkit_WM278/R_Versions/.RData]
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'rownames': bad_weak_ptr
Error: bad_weak_ptr
Loading required namespace: openCyto
> library(ncdfFlow)
Loading required package: flowCore
Loading required package: BH
> library(flowWorkspace)
As part of improvements to flowWorkspace, some behavior of
GatingSet objects has changed. For details, please read the section
titled "The cytoframe and cytoset classes" in the package vignette:
vignette("flowWorkspace-Introduction", "flowWorkspace")
> library(CytoML)
> dataDir <- system.file("extdata",package="flowWorkspaceData")
> #load raw FCS
> fs <- load_cytoset_from_fcs(file.path(dataDir,"CytoTrol_CytoTrol_1.fcs"))
> gs <- GatingSet(fs)
>
> #compensate
> comp <- spillover(fs[[1]])[["SPILL"]]
> chnls <- colnames(comp)
> comp <- compensation(comp)
> gs <- compensate(gs, comp)
>
> #transform
> trans <- flowjo_biexp_trans()
> trans <- transformerList(chnls, trans)
> gs <- transform(gs, trans)
>
> library(openCyto)
> #load the original template for tcell panel
> tbl <- data.table::fread(system.file("extdata/gating_template/tcell.csv", package = "openCyto"))
> #modify some paramters to fit the current data range
> tbl[5, gating_args:= "gate_range = c(1e3, 3e3)"]
> tbl[c(8,11), gating_args:= "gate_range = c(2e3, 3e3)"]
> #write the new template to disc
> gtFile <- tempfile()
> write.csv(tbl, file = gtFile)
> ##reload the new template
> gt <- gatingTemplate(gtFile)
expanding pop: -/++/-
expanding pop: +/-+/-
expanding pop: +/-+/-
Adding population:nonDebris
Adding population:singlets
Adding population:lymph
Adding population:cd3
Adding population:cd4+
Adding population:cd8+
Adding population:cd4+cd8+
Adding population:cd4-cd8+
Adding population:cd4+cd8-
Adding population:cd4-cd8-
Adding population:CD38+
Adding population:HLA+
Adding population:activated cd4
Adding population:CD38+
Adding population:HLA+
Adding population:activated cd8
Adding population:CD45_neg
Adding population:CCR7_gate
Adding population:CCR7+CD45RA+
Adding population:CCR7-CD45RA+
Adding population:CCR7+CD45RA-
Adding population:CCR7-CD45RA-
Adding population:CCR7+
Adding population:CD45RA+
Adding population:CCR7+CD45RA+
Adding population:CCR7-CD45RA+
Adding population:CCR7+CD45RA-
Adding population:CCR7-CD45RA-
> #run the gating
> gating(gt, gs)
Gating for 'nonDebris'
done!
done.
Gating for 'singlets'
done!
done.
Preprocessing for 'lymph'
'K' argument is missing in prior_flowclust! Using default setting: K = 2.
You should set this to the same value as 'K' in the call to flowClust.
Gating for 'lymph'
Using the serial version of flowClust
done!
done.
Gating for 'cd3'
done!
done.
Gating for 'cd8+'
done!
done.
Gating for 'cd4+'
done!
done.
Population 'cd4-cd8-'
done.
Population 'cd4+cd8-'
done.
Gating for 'CD45_neg'
done!
done.
Gating for 'CCR7_gate'
The prior specification has no effect when usePrior=no
Using the serial version of flowClust
done!
done.
Population 'CCR7-CD45RA-'
done!
done.
Population 'CCR7+CD45RA-'
done!
done.
Population 'CCR7-CD45RA+'
done!
done.
Population 'CCR7+CD45RA+'
done!
done.
Preprocessing for 'HLA+'
Gating for 'HLA+'
done!
done.
Preprocessing for 'CD38+'
Gating for 'CD38+'
done!
done.
Population 'activated cd4'
done.
Population 'cd4-cd8+'
done.
Gating for 'CD45RA+'
done!
done.
Gating for 'CCR7+'
done!
done.
Population 'CCR7-CD45RA-'
done.
Population 'CCR7+CD45RA-'
done.
Population 'CCR7-CD45RA+'
done.
Population 'CCR7+CD45RA+'
done.
Preprocessing for 'HLA+'
Gating for 'HLA+'
done!
done.
Preprocessing for 'CD38+'
Gating for 'CD38+'
done!
done.
Population 'activated cd8'
done.
Population 'cd4+cd8+'
done.
finished.
Warning messages:
1: In gating(gt, gs) : 'gating' is deprecated.
Use 'gt_gating' instead.
See help("Deprecated")
2: In getChannelMarker(parent_data[[1, use.exprs = FALSE]], channel) :
HLA is partially matched with V545-AHLA-DR V500
3: In getChannelMarker(frm, channel) :
HLA is partially matched with V545-AHLA-DR V500
4: In getChannelMarker(fr, dim) :
HLA is partially matched with V545-AHLA-DR V500
5: In getChannelMarker(parent_data[[1, use.exprs = FALSE]], channel) :
HLA is partially matched with V545-AHLA-DR V500
6: In getChannelMarker(frm, channel) :
HLA is partially matched with V545-AHLA-DR V500
7: In getChannelMarker(fr, dim) :
HLA is partially matched with V545-AHLA-DR V500
> #hide the gates that are not of interest
> toggle.helperGates(gt, gs)
Warning message:
In toggle.helperGates(gt, gs) : 'toggle.helperGates' is deprecated.
Use 'gt_toggle_helpergates' instead.
See help("Deprecated")
> #visualize the gates
> library(ggcyto)
Loading required package: ggplot2
> autoplot(gs[[1]])
Coordinate system already present. Adding new coordinate system, which will replace the
existing one.
Coordinate system already present. Adding new coordinate system, which will replace the
existing one.
Coordinate system already present. Adding new coordinate system, which will replace the
existing one.
Coordinate system already present. Adding new coordinate system, which will replace the
existing one.
Coordinate system already present. Adding new coordinate system, which will replace the
existing one.
Coordinate system already present. Adding new coordinate system, which will replace the
existing one.
Coordinate system already present. Adding new coordinate system, which will replace the
existing one.
Coordinate system already present. Adding new coordinate system, which will replace the
existing one.
Coordinate system already present. Adding new coordinate system, which will replace the
existing one.
>
> outFile <- "cytoML_CB_Ref.xml"
> gatingset_to_cytobank(gs, outFile)
[1] "cytoML_CB_Ref.xml"
There were 50 or more warnings (use warnings() to see the first 50)
>
> outFile <- "cytoML_FJ_Ref.wsp"
> gatingset_to_flowjo(gs, outFile)
INFO: Could not find files for the given pattern(s).
Using docker image public.ecr.aws/x4k5d9i7/cytoverse/gs-to-wsp:latest to write FlowJo workspace...
[1] TRUE
>
>
>
>
>
> warnings()
Warning messages:
1: In gatingset_to_cytobank(gs, outFile) :
With 'cytobank.default.scale' set to 'TRUE', data and gates will be re-transformed with cytobank's default scaling settings, which may affect how gates look like.
2: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gating
3: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gating
4: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
5: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
6: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gating
7: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
8: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
9: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gating
10: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
11: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
12: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gating
13: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
14: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
15: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gating
16: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
17: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
18: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gating
19: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
20: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
21: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gating
22: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
23: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
24: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gating
25: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
26: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
27: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gating
28: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
29: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
30: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gating
31: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
32: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
33: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gating
34: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gating
35: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gating
36: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
37: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
38: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gating
39: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
40: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
41: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gating
42: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
43: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
44: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gating
45: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
46: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
47: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gating
48: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
49: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gatingmissing namespace definitions for prefix(es) gating
50: In checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, ... :
missing namespace definitions for prefix(es) gating
> cytoverse::cytoverse_update()
Installed Available Update
RProtoBufLib 2.20.0 2.20.0
cytolib 2.20.0 2.20.0
flowCore 2.20.0 2.20.0
flowViz 1.72.0 1.72.0
ncdfFlow 2.54.0 2.54.0
flowWorkspace 4.20.0 4.20.0
flowWorkspaceData 3.20.0 3.20.0
flowClust 3.46.0 3.46.0
flowStats 4.20.0 4.20.0
ggcyto 1.36.0 1.36.0
openCyto 2.20.0 2.20.0
CytoML 2.20.0 2.20.0