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Plotting kmeansFilter in xyplot - error #256

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wptmdoorn opened this issue Aug 21, 2023 · 0 comments
Open

Plotting kmeansFilter in xyplot - error #256

wptmdoorn opened this issue Aug 21, 2023 · 0 comments

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@wptmdoorn
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Describe the bug
I am trying to apply a kmeansFilter to a flowFrame and then plot the different clusters using xyplot. According to https://www.bioconductor.org/packages/devel/bioc/vignettes/flowViz/inst/doc/filters.html this should be possible.
Filtering works, but then the xyplot produces an issue, see below.

To Reproduce
See code below.

library(ggplot2)
library(flowCore)
library(flowViz)
#> Loading required package: lattice
data(GvHD)

data <- GvHD[[1]]

kf <- flowCore::kmeansFilter(
    "SSC-H" = c("Pop1", "Pop2"),
    filterId = "myKmFilter"
)

kf.results <- flowCore::filter(data, kf)
print(summary(kf.results))
#> Pop1: 3060 of 3420 events (89.47%)
#> Pop2: 360 of 3420 events (10.53%)

flowViz::xyplot(`SSC-H` ~ `FSC-H`, data = data, filter = kf.results)

Expected behavior
I would expect the xyplot to show the different clusters.

Screenshots
The error is in the plot below. I don't why it tells me I provided it frame V1 as I supply it with data = data.
Thank you very much in advance.

sessionInfo():

> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=Dutch_Netherlands.utf8  LC_CTYPE=Dutch_Netherlands.utf8
[3] LC_MONETARY=Dutch_Netherlands.utf8 LC_NUMERIC=C
[5] LC_TIME=Dutch_Netherlands.utf8

time zone: Europe/Paris
tzcode source: internal

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

other attached packages:
[1] reprex_2.0.2     flowPeaks_1.46.0 flowViz_1.64.0   lattice_0.21-8
[5] flowCore_2.12.0  scales_1.2.1     ggplot2_3.4.2

loaded via a namespace (and not attached):
 [1] gtable_0.3.3         xfun_0.39            processx_3.8.1
 [4] latticeExtra_0.6-30  Biobase_2.60.0       callr_3.7.3
 [7] ps_1.7.5             vctrs_0.6.3          tools_4.3.1
[10] generics_0.1.3       stats4_4.3.1         tibble_3.2.1        
[13] flowWorkspace_4.12.0 fansi_1.0.4          pkgconfig_2.0.3
[16] R.oo_1.25.0          KernSmooth_2.23-21   data.table_1.14.8
[19] RColorBrewer_1.1-3   S4Vectors_0.38.1     graph_1.78.0
[22] lifecycle_1.0.3      R.cache_0.16.0       compiler_4.3.1
[25] farver_2.1.1         deldir_1.0-9         munsell_0.5.0
[28] htmltools_0.5.5      yaml_2.3.7           hexbin_1.28.3
[31] pillar_1.9.0         MASS_7.3-60          R.utils_2.12.2
[34] RProtoBufLib_2.12.0  styler_1.10.1        tidyselect_1.2.0
[37] digest_0.6.31        dplyr_1.1.2          purrr_1.0.1
[40] labeling_0.4.2       fastmap_1.1.1        grid_4.3.1
[43] colorspace_2.1-0     cli_3.6.1            magrittr_2.0.3
[46] ncdfFlow_2.46.0      XML_3.99-0.14        utf8_1.2.3
[49] clipr_0.8.0          withr_2.5.0          rmarkdown_2.23      
[52] matrixStats_1.0.0    jpeg_0.1-10          interp_1.1-4
[55] cytolib_2.12.0       png_0.1-8            R.methodsS3_1.8.2
[58] evaluate_0.21        knitr_1.43           rlang_1.1.1
[61] Rcpp_1.0.10          glue_1.6.2           Rgraphviz_2.44.0
[64] BiocManager_1.30.21  renv_0.17.3          BiocGenerics_0.46.0
[67] rstudioapi_0.15.0    jsonlite_1.8.5       R6_2.5.1
[70] IDPmisc_1.1.20       fs_1.6.2             zlibbioc_1.46.0   
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