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RGLab / openCyto

A package that provides data analysis pipeline for flow cytometry.
GNU Affero General Public License v3.0
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tmix2DGate not found #217

Closed santoshe1 closed 4 years ago

santoshe1 commented 4 years ago

I am running into errors with tmix2DGate. I have installed flowIncubator, however I could not find the tmix2DGate library/rscript when i search, please find my code below for your reference.

library(openCyto)
library(ggcyto)
library(flowIncubator)

tmix2DGate.wrapper <- function(fr, pp_res = NULL, channels, ...){
  flowIncubator:::tmix2DGate(fr, channels, ...)

}
register_plugins(tmix2DGate.wrapper, "tmix2DGate.wrapper")

gs_add_gating_method(gs, alias = "cd4,cd8"
          , pop = "*"
          , parent = "cd3"
          , dims = "cd4,cd8"
          , gating_method = "tmix2DGate.wrapper"
          , gating_args = "K = 2, quantile = 0.6, trans = 0"
          )
autoplot(gs, c("cd4", "cd8"))

Error: Error in (function (fs, pp_res, gFunc, popAlias, channels, gFunc_args) : failed at 1 Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : object 'tmix2DGate' not found 

sessionInfo()
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /apps/miniconda/envs/R4/lib/libopenblasp-r0.3.10.so

locale:
 [1] LC_CTYPE=en_US       LC_NUMERIC=C         LC_TIME=en_US
 [4] LC_COLLATE=en_US     LC_MONETARY=en_US    LC_MESSAGES=en_US
 [7] LC_PAPER=en_US       LC_NAME=C            LC_ADDRESS=C
[10] LC_TELEPHONE=C       LC_MEASUREMENT=en_US LC_IDENTIFICATION=C

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

other attached packages:
 [1] flowIncubator_0.99.10     devtools_2.3.1
 [3] usethis_1.6.1             flowDensity_1.22.0
 [5] flowAI_1.18.5             gridExtra_2.3
 [7] flowClean_1.26.0          scales_1.1.1
 [9] Biobase_2.48.0            BiocGenerics_0.34.0
[11] flowStats_4.0.0           data.table_1.13.0
[13] CytoML_2.0.5              openCyto_2.0.0
[15] flowTrans_1.40.0          flowClust_3.26.0
[17] flowViz_1.52.0            lattice_0.20-41
[19] ggcyto_1.16.0             flowWorkspace_4.0.6
[21] ncdfFlow_2.34.0           BH_1.72.0-3
[23] RcppArmadillo_0.9.900.2.0 ggplot2_3.3.2
[25] flowCore_2.0.1            BiocManager_1.30.10

Kindly assist. Thanks

gfinak commented 4 years ago

If I type tmix2DGate and GitHub into Google, my first result shows me that it was moved into CytoUtils at least as far back as 2017. Maybe try looking there.