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Describe the bug
A newly constructed flowFrame has no keywords.
When written to an FCS file using write.FCS, some default keywords are set, but the file can't be properly read and displayed in FlowJo because keyword values don't reflect the underlying data.
To Reproduce
library(flowCore)
#> Warning: package 'flowCore' was built under R version 3.5.1
m <- matrix(rnorm(1000),ncol=4)
colnames(m) <- LETTERS[1:4]
fr <- flowFrame(m)
keyword(fr)
#> list() #at this point there are no keywords.
write.FCS(fr,filename = file.path("/tmp/test.fcs")) #keywords are added on write.FCS.
#> [1] "/tmp/test.fcs"
system(paste0("open /tmp"))
# open FlowJo and drag the fcs file to the workspace.
# The file does not display properly. (see screenshot)
keyword(read.FCS("/tmp/test.fcs"))["$P1R"]
#> $`$P1R`
#> [1] "1024" #note this range doesn't reflect the underlying data.
# The keywords for the range are set to a default value, but should be updated on object creation
# to reflect the range of the data.
Expected behavior
A newly created flowFrame via the flowFrame() constructor should have range (and maybe other keywords) set to reflect the contents of the data frame.
Screenshots
No events are visible due to the range of display (taken from the keywords, presumably)
sessionInfo():
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6
range is fixed during write.FCS.
But I can only set maximum value through $PnR, to display those negative values linear scaling needs to be manually adjusted in flowJo
Describe the bug
A newly constructed flowFrame has no keywords.
When written to an FCS file using write.FCS, some default keywords are set, but the file can't be properly read and displayed in FlowJo because keyword values don't reflect the underlying data.
To Reproduce
Created on 2018-08-24 by the reprex
package (v0.2.0).
Expected behavior
A newly created flowFrame via the
flowFrame()
constructor should have range (and maybe other keywords) set to reflect the contents of the data frame.Screenshots
No events are visible due to the range of display (taken from the keywords, presumably)
sessionInfo():
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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] flowCore_1.47.5
loaded via a namespace (and not attached):
[1] pcaPP_1.9-73 Rcpp_0.12.18 DEoptimR_1.0-8 compiler_3.5.0
[5] tools_3.5.0 digest_0.6.15 memoise_1.1.0 evaluate_0.11
[9] lattice_0.20-35 rlang_0.2.2 reprex_0.2.0 graph_1.59.0
[13] rstudioapi_0.7 yaml_2.2.0 parallel_3.5.0 mvtnorm_1.0-8
[17] knitr_1.20 withr_2.1.2 stringr_1.3.1 cluster_2.0.7-1
[21] devtools_1.13.6 stats4_3.5.0 rprojroot_1.3-2 grid_3.5.0
[25] robustbase_0.93-2 Biobase_2.41.2 rrcov_1.4-4 R6_2.2.2
[29] processx_3.2.0 rmarkdown_1.10 magrittr_1.5 callr_2.0.4
[33] corpcor_1.6.9 clipr_0.4.1 whisker_0.3-2 backports_1.1.2
[37] ps_1.1.0 matrixStats_0.54.0 htmltools_0.3.6 MASS_7.3-50
[41] BiocGenerics_0.27.1 assertthat_0.2.0 stringi_1.2.4 crayon_1.3.4
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