Question: RefGate populations switched in OpenCyto 1.20
gravatar for k.teijgeler
11 months ago by
k.teijgeler0 wrote:

Recently I started converting my gating template from OpenCyto 1.14 to OpenCyto 1.20. Currently i am running in to the following problem (see picture below).
The populations are swapped:
+- = --
-- = +-
++ = -+
-+ = ++

Swapped populations in ReferenceGate


I am using a csv file as gating file, with the below arguments:

alias pop parent dims gating_method gating_args collapseDataForGating groupBy preprocessing_method preprocessing_args
CD4+FoxP3+ + CD4+ PE.Texas.Red.A tailgate min = -0.5, max = 1.35, tol = 0.15 TRUE PID    
CD4+FoxP3- - CD4+ PE.Texas.Red.A refGate CD4+FoxP3+        
CD4+IL17+ + CD4+ BV711.A tailgate num_peaks = 5 , ref_peak = 5 , strict = FALSE , min = -0.5, max = 1.75,  tol = 0.01 TRUE PID    
CD4+IL17- + CD4+ BV711.A refGate CD4+IL17+        
CD4+FoxP3-IL17- -- CD4+ PE.Texas.Red.A,BV711.A refGate CD4+FoxP3-:CD4+IL17-        
CD4+FoxP3-IL17+ -+ CD4+ PE.Texas.Red.A,BV711.A refGate CD4+FoxP3-:CD4+IL17-        
CD4+FoxP3+IL17- +- CD4+ PE.Texas.Red.A,BV711.A refGate CD4+FoxP3-:CD4+IL17-        
CD4+FoxP3+IL17+ ++ CD4+ PE.Texas.Red.A,BV711.A refGate



Any idea what might be causing this, or in which direction i should look for a solution :)?

 Session Info:

R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.5 (Maipo)

Matrix products: default
BLAS: /opt/R/3.5.1/lib64/R/lib/
LAPACK: /opt/R/3.5.1/lib64/R/lib/

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              

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

other attached packages:
 [1] bindrcpp_0.2.2            DT_0.5                    openxlsx_4.1.0           
 [4] rhandsontable_0.3.7       reshape2_1.4.3            tidyr_0.8.2              
 [7] dplyr_0.7.8               plyr_1.8.4                flowViz_1.46.0           
[10] lattice_0.20-38           flowAI_1.12.1             flowDensity_1.16.0       
[13] flowStats_3.40.0          cluster_2.0.7-1           flowClust_3.20.0         
[16] openCyto_1.20.0           flowWorkspace_3.28.3      ncdfFlow_2.28.0          
[19] BH_1.66.0-1               RcppArmadillo_0. flowCore_1.48.0          
[22] shiny_1.2.0              

loaded via a namespace (and not attached):
  [1] colorspace_1.3-2    rio_0.5.16          rsconnect_0.8.12    mclust_5.4.2        rprojroot_1.3-2    
  [6] corpcor_1.6.9       fs_1.2.6            clue_0.3-56         rstudioapi_0.8      hexbin_1.27.2      
 [11] IDPmisc_1.1.18      mvtnorm_1.0-8       splines_3.5.1       R.methodsS3_1.7.1   mnormt_1.5-5       
 [16] robustbase_0.93-3   knitr_1.20          jsonlite_1.5        spam_2.2-0          rgeos_0.4-2        
 [21] R.oo_1.22.0         RPMG_2.2-2          graph_1.60.0        rrcov_1.4-7         compiler_3.5.1     
 [26] backports_1.1.2     lazyeval_0.2.1      assertthat_0.2.0    Matrix_1.2-15       later_0.7.5        
 [31] htmltools_0.3.6     tools_3.5.1         dotCall64_1.0-0     Rwave_2.4-8         gtable_0.2.0       
 [36] glue_1.3.0          maps_3.3.0          Rcpp_1.0.0          carData_3.0-2       Biobase_2.42.0     
 [41] cellranger_1.1.0    gdata_2.18.0        crosstalk_1.0.0     RFOC_3.4-6          changepoint_2.2.2  
 [46] stringr_1.3.1       mime_0.6            gtools_3.8.1        XML_3.98-1.16       DEoptimR_1.0-8     
 [51] zoo_1.8-4           zlibbioc_1.28.0     MASS_7.3-51.1       scales_1.0.0        hms_0.4.2          
 [56] promises_1.0.1      RBGL_1.58.1         RColorBrewer_1.1-2  fields_9.6          yaml_2.2.0         
 [61] curl_3.2            MBA_0.0-9           gridExtra_2.3       ggplot2_3.1.0       latticeExtra_0.6-28
 [66] stringi_1.2.4       pcaPP_1.9-73        caTools_1.17.1.1    BiocGenerics_0.28.0 zip_1.0.0          
 [71] rlang_0.3.0.1       pkgconfig_2.0.2     matrixStats_0.54.0  bitops_1.0-6        evaluate_0.12      
 [76] fda_2.4.8           purrr_0.2.5         bindr_0.1.1         htmlwidgets_1.3     ks_1.11.3          
 [81] tidyselect_0.2.5    magrittr_1.5        R6_2.3.0            gplots_3.0.1        pillar_1.3.0       
 [86] haven_2.0.0         foreign_0.8-71      abind_1.4-5         sp_1.3-1            tibble_1.4.2       
 [91] crayon_1.3.4        car_3.0-2           shinyFiles_0.7.2    GEOmap_2.4-4        KernSmooth_2.23-15 
 [96] ellipse_0.4.1       rmarkdown_1.10      grid_3.5.1          readxl_1.1.0        data.table_1.11.8  
[101] Rgraphviz_2.26.0    forcats_0.3.0       splancs_2.01-40     digest_0.6.18       xtable_1.8-3       
[106] httpuv_1.4.5        R.utils_2.7.0       stats4_3.5.1        munsell_0.5.0       shinyjs_1.0        
[111] RSEIS_3.8-3        
opencyto refgate • 255 views
ADD COMMENTlink modified 10 months ago by Jiang, Mike1.2k • written 11 months ago by k.teijgeler0

refGate seems to work fine for me. See and try to run it to check if you can reproduce it.

I can do some more testing(by mimic the same pop names as yours) If you can confirm your issue remains in your particular use case but can run my example without problems.

ADD REPLYlink written 11 months ago by Jiang, Mike1.2k

Thanks for the quick reply, i have checked your rpub and that works fine for me. None of the populations are switched there.

Would be great if could do some more testing. Please tell me if you need more information.

ADD REPLYlink written 11 months ago by k.teijgeler0

Hi Mike,

Did you have a chance to look at this?

ADD REPLYlink written 11 months ago by k.teijgeler0

I have tried to modify the population names to simulate your use case but it still works fine for me. I think you will have to provide a minimal reproducible example in order for me to troubleshoot it.

ADD REPLYlink modified 11 months ago • written 11 months ago by Jiang, Mike1.2k

Could you mail me at, then i send you are more complete gatingfile

ADD REPLYlink written 10 months ago by k.teijgeler0
Answer: RefGate populations switched in OpenCyto 1.20
gravatar for Jiang, Mike
10 months ago by
Jiang, Mike1.2k
(Private Address)
Jiang, Mike1.2k wrote:

I've pushed the fix. See details You can either install the development version from github or wait for the updated release build 1.20.2 from BioC site(which typically takes 1 or 2 days to appear).

ADD COMMENTlink written 10 months ago by Jiang, Mike1.2k

Thanks a lot Mike for the quick solution! :)

ADD REPLYlink written 10 months ago by k.teijgeler0
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