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RGLab / CytoML

A GatingML Interface for Cross Platform Cytometry Data Sharing
GNU Affero General Public License v3.0
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After updating to CytoML_2.0.5, error in flowjo_to_gatingset if path is a data.frame #112

Open PedroMilanezAlmeida opened 4 years ago

PedroMilanezAlmeida commented 4 years ago

In flowjo_to_gatingset, for some reason, I cannot use a data.frame as path anymore.

After some digging, it looks like flowjo_to_gatingset runs , path = suppressWarnings(normalizePath(path)) directly on the path, throwing an Error in path.expand(path) : invalid 'path' argument if path is a data.frame.

Is this only happening to me?

PS: I need to parse the FJ-wsp file always only one sample at a time. I used to be able to provide a data.frame with one row (just the sample of interest) and column names "sampleID" and "file" but that does not seem to work anymore.

Any help would be much appreciated.

EDIT:

sessionInfo()

R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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] CytoML_2.0.5        flowWorkspace_4.0.6

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5          plyr_1.8.6          compiler_4.0.2      pillar_1.4.6       
 [5] cytolib_2.0.3       RColorBrewer_1.1-2  base64enc_0.1-3     tools_4.0.2        
 [9] zlibbioc_1.34.0     digest_0.6.25       jsonlite_1.7.0      gtable_0.3.0       
[13] lifecycle_0.2.0     tibble_3.0.3        lattice_0.20-41     pkgconfig_2.0.3    
[17] png_0.1-7           rlang_0.4.7         graph_1.66.0        rstudioapi_0.11    
[21] Rgraphviz_2.32.0    yaml_2.2.1          parallel_4.0.2      hexbin_1.28.1      
[25] gridExtra_2.3       xml2_1.3.2          stringr_1.4.0       dplyr_1.0.1        
[29] generics_0.0.2      vctrs_0.3.2         stats4_4.0.2        grid_4.0.2         
[33] tidyselect_1.1.0    glue_1.4.1          data.table_1.13.0   Biobase_2.48.0     
[37] R6_2.4.1            jpeg_0.1-8.1        RBGL_1.64.0         XML_3.99-0.5       
[41] latticeExtra_0.6-29 ggplot2_3.3.2       RProtoBufLib_2.0.0  purrr_0.3.4        
[45] magrittr_1.5        scales_1.1.1        matrixStats_0.56.0  ellipsis_0.3.1     
[49] BiocGenerics_0.34.0 colorspace_1.4-1    flowCore_2.0.1      ncdfFlow_2.34.0    
[53] stringi_1.4.6       RcppParallel_5.0.2  munsell_0.5.0       crayon_1.3.4       
[57] ggcyto_1.16.0
PedroMilanezAlmeida commented 4 years ago

https://github.com/RGLab/CytoML/issues/113#issuecomment-679213641

gfinak commented 4 years ago

Thanks for pointing this out. I suspect the data.frame support was silently dropped in the changeover.

mikejiang commented 4 years ago

Right, data.frame historically allow users to manually provide the mapping between flowJo sampleID and fcs file path for each sample when the automated matching failed to match them up (mostly due to the renaming fcs files at some point). But we've introduced a more robust fcs searching method ever since, which matches both file name and keyword contents and pretty much resolved that issue. So, this functionality is currently dropped. Unless you can provide a compelling reason to restore such feature.

PedroMilanezAlmeida commented 4 years ago

https://github.com/RGLab/CytoML/issues/113#issuecomment-680044846