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k.teijgeler
•
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@kteijgeler-15773
Last seen 5.3 years ago
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:
+- = --
-- = +-
++ = -+
-+ = ++
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 |
CD4+FoxP3-:CD4+IL17- |
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/libRblas.so LAPACK: /opt/R/3.5.1/lib64/R/lib/libRlapack.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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_0.9.200.5.0 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
refGate seems to work fine for me. See http://rpubs.com/wjiang2/453106 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.
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.
Hi Mike,
Did you have a chance to look at this?
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.
Could you mail me at kteijgel@its.jnj.com, then i send you are more complete gatingfile