Week #5 - General Discussion Thread

[UMGCCCFCSR]

This is the General Discussion post for Week # 5 - Gating Sets.

• Wondering what other differences exist between flowFrame and cytoFrames?
• Curious about why the choice of flowFrame/cytoFrame use for a particular R package can elicit some flow cytometry developer drama?
• Troubleshooting a scaling bug in the Floreada-CytoML import?

If it doesn't rise to the level where it merits its own Q&A threaad, this post is the place for you!

[njjacobs]

OperatingSystem <- Sys.info()[["sysname"]]
+

• if (OperatingSystem == "Windows") { # Windows

• memory.limit()
  

• } else if (OperatingSystem == "Darwin") { # MacOS

• system("top -l 1 | grep PhysMem")
  

• } else if (OperatingSystem == "Linux") { # Linux

• system("free -h")
  

• } else {message("A wild FreeBSD-User appears")}
  Warning message:
  'memory.limit()' is no longer supported
  [1] Inf

I have Windows and when I enter this code I get a warning saying memory.limit() is no longer supported. Is that going to be an issue moving forward?

[DavidRach]

Thanks for spotting @njjacobs, I will update with the correct non-deprecated version

[DavidRach]

@njjacobs, revised to use a ps R package function (trying to substitute the deprecated memory.limit() with a system level call was too convoluted). Thanks for noticing it! Best- David

# install.packages("ps") # CRAN
library(ps)
Memory <- ps::ps_system_memory()
message("Total GB ", round(Memory$total / 1024^3, 2))
message("Free GB ", round(Memory$free / 1024^3, 2))

[A-hedgecock-Flowcore]

Having issues rendering my Qurato doc. When I execute the Code chucks by themselves or use the "Run Above" option, I dont have any issues. Whenever I try to render the doc, I keep geting the below error message. I've restarted Postiron and cleared my enviroment to try to redo it but I'm still having issues.

quarto preview /Users/ayrianna/Documents/Week5/A-hedgecock-FlowCore/Homework.qmd --no-browser --no-watch-inputs
ayrianna@Ayriannas-Laptop-2 Week5 % quarto preview /Users/ayri
anna/Documents/Week5/A-hedgecock-FlowCore/Homework.qmd --no-br
owser --no-watch-inputs

processing file: Homework.qmd
1/16
2/16 [Call libraries]
3/16
4/16 [File paths]
5/16
6/16 [unnamed-chunk-1]
Error:
! Expected string vector of length 1
Backtrace:
▆

1. └─CytoML::open_flowjo_xml(OpenedWorkspace)
2. ├─methods::new(...)
3. │ ├─methods::initialize(value, ...)
4. │ └─methods::initialize(value, ...)
5. └─CytoML:::open_workspace(...)

Quitting from Homework.qmd:33-36 [unnamed-chunk-1]
Execution halted
WARN: Error encountered when rendering files
ayrianna@Ayriannas-Laptop-2 Week5 %

ChatGPT was trying to help diagnose, so this may be helpful:

getwd()
[1] "/Users/ayrianna/Documents/Week5"
print(DataFolder)
[1] "A-hedgecock-FlowCore/data"
print(dir.exists(DataFolder))
[1] TRUE
print(FlowJoWspFiles)
[1] "A-hedgecock-FlowCore/data/FlowJoWSP_OpenedCopy.wsp"
[2] "A-hedgecock-FlowCore/data/FlowJoWSP_Unopened.wsp"
print(OpenedWorkspace)
[1] "A-hedgecock-FlowCore/data/FlowJoWSP_OpenedCopy.wsp"
print(length(OpenedWorkspace))
[1] 1
str(OpenedWorkspace)
chr "A-hedgecock-FlowCore/data/FlowJoWSP_OpenedCopy.wsp"
class(OpenedWorkspace)
[1] "character"

sessionInfo()
R version 4.5.2 (2025-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Tahoe 26.2

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats graphics grDevices utils datasets
[6] methods base

other attached packages:
[1] dplyr_1.2.0 CytoML_2.22.0
[3] ggcyto_1.39.1 ncdfFlow_2.56.0
[5] BH_1.90.0-1 ggplot2_4.0.2
[7] flowWorkspace_4.22.1 flowCore_2.22.1

loaded via a namespace (and not attached):
[1] jsonlite_2.0.0 gtable_0.3.6
[3] compiler_4.5.2 Rcpp_1.1.1
[5] tidyselect_1.2.1 Biobase_2.70.0
[7] stringr_1.6.0 cytolib_2.22.0
[9] gridExtra_2.3 Rgraphviz_2.54.0
[11] scales_1.4.0 yaml_2.3.12
[13] lattice_0.22-9 plyr_1.8.9
[15] hexbin_1.28.5 R6_2.6.1
[17] RProtoBufLib_2.22.0 generics_0.1.4
[19] RBGL_1.86.0 BiocGenerics_0.56.0
[21] graph_1.88.1 XML_3.99-0.22
[23] tibble_3.3.1 pillar_1.11.1
[25] RColorBrewer_1.1-3 rlang_1.1.7
[27] stringi_1.8.7 S7_0.2.1
[29] cli_3.6.5 withr_3.0.2
[31] magrittr_2.0.4 grid_4.5.2
[33] lifecycle_1.0.5 S4Vectors_0.48.0
[35] vctrs_0.7.1 glue_1.8.0
[37] data.table_1.18.2.1 farver_2.1.2
[39] stats4_4.5.2 matrixStats_1.5.0
[41] tools_4.5.2 pkgconfig_2.0.3

[DavidRach]

Hi @A-hedgecock-Flowcore, Quarto is finicky about it's working environment when rendering, so it's likely one your file paths is slightly off for what it should be. You may have noticed the following this week:

I keep one file path # when working in the .qmd, and then silence it and remove the # from the other when rendering.

You can try to debug by running the code all the way up before CytoML function is run, and add a getwd(). Silence all code chunks below that point for now by setting eval: FALSE. That should allow the document to finish rendering, and you can identify the file path difference right before CytoML step.

Mid sorter meltdown at the moment, so will be back when I can.

Best-
David

[A-hedgecock-Flowcore]

Ahh, that was it. I had to change the file.path() to just "data"

Thanks and hope the sorter is alright!

[mattz63]

I'm having trouble creating the flowSet object. It seems like the code is successful:

read.flowSet (files=fcs_files[c(1, 3:4)], truncate_max_range = FALSE, transformation = FALSE)
A flowSet with 3 experiments.

column names(43): Time SSC-W ... APC-Fire 810-A AF-A

But the flowSet object does not appear in the right window under "Values". This is what does appear to this point:

[DavidRach]

Hi @mattz63, you will need to add an assignment arrow and a variable/object name to that line of code 🙂

flowSet <-

Some of the code example lines on the website skip that step when just showing object internals, you will notice the object ends up getting created on the next code chunk.

Best-
David

[claude-chew]

Hi @DavidRach,

So I was banging my head against a wall trying to plot the TNFa vs IFNg data for the samples. It looks like only 2 of the samples have these column names, correct? Do you want us to harmonize axes/parameters and plot data for all 6 samples?

Thanks,
Claude

[claude-chew]

Nevermind, figured it out, I with Copilot's help I had to tell pData to use unique sample names and plot using the actual parameter labels