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RGLab / openCyto

A package that provides data analysis pipeline for flow cytometry.
GNU Affero General Public License v3.0
77 stars 29 forks source link

gate_mindensity_2( ) unable to find valleys even if gate_range() or min/max specified #246

Open maximesunnen opened 1 year ago

maximesunnen commented 1 year ago 
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")

matrix <- matrix(c(17.1702575683594, 3604.7919921875, 4885.357421875, 3255.04663085938, 
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                   27.4206047058105, 20.3002529144287, 6511.591796875, 1938.85754394531, 
                   63.1950569152832, 29.4188671112061, 4699.26318359375, 4500.4794921875, 
                   24.6113185882568, 37.6647834777832, 6367.029296875, 37.6647834777832, 
                   8111.38623046875, 11491.1513671875, 467.405364990234, 8745.119140625, 
                   5541.6142578125, 89.3667526245117, 4512.3857421875, 4055.10400390625, 
                   25.1078014373779, 85.5860824584961, 27.8708305358887, 4852.23193359375, 
                   3613.23510742188, 3437.36352539062, 57.564151763916, 38.3062019348145, 
                   8122.19482421875, 1878.92504882812, 33.5264091491699, 6972.00341796875, 
                   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_4.2.2

Created on 2023-04-10 with reprex v2.0.2

djhammill commented 2 weeks ago

@maximesunnen the outputs look correct to me, we can try to help if you provide additional context or explanation of the expected result in each case.

maximesunnen commented 6 days ago

@djhammill so for you the minimum is located at the intersection of the red and black line in the last 2 plots? The valley is located more on the left for me.

djhammill commented 4 days ago

Mindensity uses adjust = 2 while geom_smooth uses adjust = 1 for the kernel density estimates. I suspect that if you set geom_density(adjust = 2) the locations will line up better.