gate_mindensity_2( ) unable to find valleys even if gate_range() or min/max specified #246
Description
library(openCyto)
library(ggcyto)
#> Loading required package: ggplot2
#> Loading required package: flowCore
#> Loading required package: ncdfFlow
#> Loading required package: BH
#> Loading required package: 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")
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11183.2646484375, 115.757385253906, 804.186645507812, 7572.505859375,
1579.259765625, 584.991394042969, 16.2204666137695, 3478.8798828125,
3040.603515625, 19.3967170715332, 4451.7470703125, 3440.92822265625,
1600.72863769531), ncol = 1
)
colnames(matrix) <- "SSC-H"
fr <- flowFrame(exprs = matrix)
test_gate_1 <- gate_mindensity2(fr, channel = "SSC-H")
ggcyto(fr, aes(x = "SSC-H")) +
geom_density() +
geom_gate(test_gate_1)
test_gate_2 <- gate_mindensity2(fr, channel = "SSC-H", gate_range = c(0,5000))
ggcyto(fr, aes(x = "SSC-H")) +
geom_density() +
geom_gate(test_gate_2)
test_gate_3 <- gate_mindensity2(fr, channel = "SSC-H", min = 0, max = 5000)
ggcyto(fr, aes(x = "SSC-H")) +
geom_density() +
geom_gate(test_gate_3)
sessionInfo()
#> R version 4.2.2 (2022-10-31)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur ... 10.16
#>
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
#>
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] ggcyto_1.26.4 flowWorkspace_4.10.1 ncdfFlow_2.44.0
#> [4] BH_1.81.0-1 flowCore_2.10.0 ggplot2_3.4.2
#> [7] openCyto_2.10.1
#>
#> loaded via a namespace (and not attached):
#> [1] tidyselect_1.2.0 xfun_0.38 lattice_0.21-8
#> [4] colorspace_2.1-0 vctrs_0.6.1 generics_0.1.3
#> [7] htmltools_0.5.5 stats4_4.2.2 yaml_2.3.7
#> [10] utf8_1.2.3 XML_3.99-0.14 RBGL_1.74.0
#> [13] rlang_1.1.0 hexbin_1.28.3 pillar_1.9.0
#> [16] glue_1.6.2 withr_2.5.0 DBI_1.1.3
#> [19] Rgraphviz_2.42.0 BiocGenerics_0.44.0 RColorBrewer_1.1-3
#> [22] plyr_1.8.8 matrixStats_0.63.0 lifecycle_1.0.3
#> [25] zlibbioc_1.44.0 RProtoBufLib_2.10.0 munsell_0.5.0
#> [28] gtable_0.3.3 cytolib_2.10.1 evaluate_0.20
#> [31] labeling_0.4.2 Biobase_2.58.0 knitr_1.42
#> [34] fastmap_1.1.1 flowClust_3.36.1 parallel_4.2.2
#> [37] fansi_1.0.4 Rcpp_1.0.10 scales_1.2.1
#> [40] S4Vectors_0.36.2 graph_1.76.0 farver_2.1.1
#> [43] fs_1.6.1 gridExtra_2.3 digest_0.6.31
#> [46] dplyr_1.1.1 grid_4.2.2 cli_3.6.1
#> [49] tools_4.2.2 magrittr_2.0.3 tibble_3.2.1
#> [52] pkgconfig_2.0.3 data.table_1.14.8 reprex_2.0.2
#> [55] rmarkdown_2.21 rstudioapi_0.14 R6_2.5.1
#> [58] compiler_4.2.2Created on 2023-04-10 with reprex v2.0.2