mikejiang
commented
3 years ago cytoset should work
> cs <- load_cytoset_from_fcs(files = file_list, emptyValue = FALSE, alter.names = TRUE)
> gs <- GatingSet(cs)The reason you see these empty s4 slots contents is because these are inherited from flowSet s4 class and not actually used by cytoset. So the real data structures are hidden behind the external pointer (in c++), i.e.
> cs@pointer
<pointer: 0x56356e303f60>and can be accessed by the cytoset accessors (i.e. s4 methods)
> cs
A cytoset with 2 samples.
column names:
FSC-HLin, SSC-HLin, GRN-HLog, YEL-HLog, RED-HLog, NIR-HLog, RED2-HLog, NIR2-HLog, FSC-HLog, SSC-HLog, GRN-HLin, YEL-HLin, RED-HLin, NIR-HLin, RED2-HLin, NIR2-HLin, NIR2-A, NIR2-ALog, NIR2-W
> cs[[1]]
cytoframe object 'C2210_CD5_CD45_CD14.fcs'
with 9310 cells and 19 observables:
name desc range minRange maxRange
$P1 FSC-HLin Forward Scatter (FSC.. 1023 0.00000 1023
$P2 SSC-HLin Side Scatter (SSC-HL.. 1023 0.00000 1023
$P3 GRN-HLog Green Fluorescence (.. 10000 1.00904 10000
$P4 YEL-HLog Yellow Fluorescence .. 10000 1.00904 10000
$P5 RED-HLog Red Fluorescence (RE.. 10000 1.00904 10000
... ... ... ... ... ...
$P15 RED2-HLin Red2 Fluorescence (R.. 1023 0 1023
$P16 NIR2-HLin Near IR2 (NIR2-HLin) 1023 0 1023
$P17 NIR2-A Near IR2 Area (NIR2-A) 1023 0 1023
$P18 NIR2-ALog Near IR2 Area (NIR2-.. 1023 0 1023
$P19 NIR2-W Near IR2 Width (NIR2.. 1023 0 1023
318 keywords are stored in the 'description' slot
row names(0):I know it maybe confusing but s4 slots are not supposed to be accessed directly by user anyway.
ghost
Hi Mike, Greg and the team, I am having a very similar issue as issue 341 but the solution of install newer version of cytolib and flowWorkspace and flowCore doesn't seem to fix the issue.
I can create flowset without problem using read.flowset() but the GatingSet is returning an error. `
in addition, (this might be related?), if I start from a cytoset with load_cytoset_from_fcs() return an empty cytoSet... using:
cs <- load_cytoset_from_fcs(files = file_list, emptyValue = FALSE, alter.names = TRUE)The FCS files that I am trying to analyze were created with a guava (FCS version 2.0). Here is an example of the file (2x) I used: Archive.zip Here is the session info():
`> sessionInfo() R version 4.1.0 (2021-05-18) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 11.5.2
Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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] flowWorkspace_4.5.3 flowCore_2.5.0 cytolib_2.5.3
loaded via a namespace (and not attached): [1] Rcpp_1.0.7 RColorBrewer_1.1-2 compiler_4.1.0 pillar_1.6.2
[5] base64enc_0.1-3 tools_4.1.0 zlibbioc_1.38.0 aws.s3_0.3.21
[9] digest_0.6.27 lattice_0.20-44 lifecycle_1.0.0 tibble_3.1.4
[13] png_0.1-7 pkgconfig_2.0.3 rlang_0.4.11 graph_1.70.0
[17] DBI_1.1.1 Rgraphviz_2.36.0 curl_4.3.2 parallel_4.1.0
[21] httr_1.4.2 dplyr_1.0.7 xml2_1.3.2 generics_0.1.0
[25] S4Vectors_0.30.0 vctrs_0.3.8 stats4_4.1.0 grid_4.1.0
[29] tidyselect_1.1.1 glue_1.4.2 data.table_1.14.0 Biobase_2.52.0
[33] R6_2.5.1 jpeg_0.1-9 fansi_0.5.0 XML_3.99-0.7
[37] latticeExtra_0.6-29 purrr_0.3.4 RProtoBufLib_2.4.0 magrittr_2.0.1
[41] scales_1.1.1 matrixStats_0.60.1 ellipsis_0.3.2 BiocGenerics_0.38.0 [45] assertthat_0.2.1 colorspace_2.0-2 aws.signature_0.6.0 ncdfFlow_2.38.0
[49] utf8_1.2.2 munsell_0.5.0 RcppParallel_5.1.4 crayon_1.4.1 `
Hope this help! Let me know if you need more information or if I missed anything in the previous issues.
Best, Stephane