READ THIS BEFORE YOU OPEN AN ISSUE
ASK YOURSELF THESE QUESTIONS
-
Do you understand your error message? Yes.
-
Have you read the documentation? Yes.
-
Have you searched existing closed issues? Yes.
-
Have you searched the Bioconductor support site? Yes.
-
Are your packages up to date? No. However, looking at the current source code and tracing back, I do not believe it is fixed.
Describe the bug
A pData<- assignment to a cytoset cannot take a data.frame with unnamed rows.
To Reproduce
I apologize: I do not currently have the bandwidth to reprex. I can provide an example, but there needs to be at least one FCS file for it to be reproduced:
METADATA <- tribble(
~filename, ~dummy,
"workspace/20250404-FCS-endocytosis-assay-2/Experiment 90_B1 3.fcs", "A") %>%
as.data.frame() %>%
AnnotatedDataFrame()
load_cytoset_from_fcs(
phenoData=METADATA, file_col_name="filename")This produces an error,
Error: Invalid input type, expected 'character' actual 'integer'
The traceback is,
> traceback()
4: set_pheno_data(object@pointer, value)
3: `pData<-`(`*tmp*`, value = pd)
2: `pData<-`(`*tmp*`, value = pd)
1: load_cytoset_from_fcs(phenoData = METADATA, file_col_name = "filename")
Expected behavior
Because load_cytoset_from_fcs does not specify that the phenoData must have named pData rows, I expect there to be no error.
Setting row names for the pData fixes this.
METADATA <- tribble(
~filename, ~sample,
"workspace/20250404-FCS-endocytosis-assay-2/Experiment 90_B1 3.fcs", "B1 3") %>%
as.data.frame() %>%
AnnotatedDataFrame()
row.names(pData(METADATA)) <- METADATA$sample
load_cytoset_from_fcs(
phenoData=METADATA, file_col_name="filename",
)Screenshots
If applicable, add screenshots to help explain your problem.
SessionInfo:
> sessionInfo()
R version 4.4.3 (2025-02-28)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Biobase_2.66.0 BiocGenerics_0.52.0 shiny_1.10.0
[4] lubridate_1.9.4 forcats_1.0.0 stringr_1.5.1
[7] dplyr_1.1.4 purrr_1.0.4 readr_2.1.5
[10] tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.1
[13] tidyverse_2.0.0 CytoExploreR_1.1.0 openCyto_2.18.0
[16] flowWorkspace_4.18.1 flowCore_2.18.0
loaded via a namespace (and not attached):
[1] changepoint_2.3 tidyselect_1.2.1 fastmap_1.2.0
[4] EmbedSOM_2.2 promises_1.3.2 XML_3.99-0.18
[7] digest_0.6.37 rsvd_1.0.5 timechange_0.3.0
[10] mime_0.13 lifecycle_1.0.4 magrittr_2.0.3
[13] compiler_4.4.3 rlang_1.1.5 sass_0.4.9
[16] tools_4.4.3 yaml_2.3.10 data.table_1.17.0
[19] knitr_1.50 askpass_1.2.1 htmlwidgets_1.6.4
[22] reticulate_1.42.0 plyr_1.8.9 RColorBrewer_1.1-3
[25] Rtsne_0.17 withr_3.0.2 RProtoBufLib_2.18.0
[28] grid_4.4.3 stats4_4.4.3 xtable_1.8-4
[31] colorspace_2.1-1 flowAI_1.36.0 scales_1.3.0
[34] MASS_7.3-64 cli_3.6.4 rmarkdown_2.29
[37] ncdfFlow_2.52.1 generics_0.1.3 umap_0.2.10.0
[40] rstudioapi_0.17.1 robustbase_0.99-4-1 RSpectra_0.16-2
[43] tzdb_0.5.0 reshape2_1.4.4 visNetwork_2.1.2
[46] cachem_1.1.0 parallel_4.4.3 rhandsontable_0.3.8
[49] matrixStats_1.5.0 vctrs_0.6.5 Matrix_1.7-2
[52] jsonlite_2.0.0 cytolib_2.18.2 hms_1.1.3
[55] S4Vectors_0.44.0 RBGL_1.82.0 Rgraphviz_2.50.0
[58] jquerylib_0.1.4 glue_1.8.0 DEoptimR_1.1-3-1
[61] stringi_1.8.7 gtable_0.3.6 later_1.4.1
[64] munsell_0.5.1 pillar_1.10.1 htmltools_0.5.8.1
[67] openssl_2.3.2 graph_1.84.1 R6_2.6.1
[70] evaluate_1.0.3 lattice_0.22-6 png_0.1-8
[73] memoise_2.0.1 httpuv_1.6.15 bslib_0.9.0
[76] Rcpp_1.0.14 flowClust_3.44.0 xfun_0.52
Additional context
Apologies again that I did not fulfil all the requirements for the issue. I thought it best to report the issue in part, rather than give up saying anything about it.
READ THIS BEFORE YOU OPEN AN ISSUE
ASK YOURSELF THESE QUESTIONS
Do you understand your error message? Yes.
Have you read the documentation? Yes.
Have you searched existing closed issues? Yes.
Have you searched the Bioconductor support site? Yes.
Are your packages up to date? No. However, looking at the current source code and tracing back, I do not believe it is fixed.
Describe the bug
A
pData<-assignment to a cytoset cannot take a data.frame with unnamed rows.To Reproduce
I apologize: I do not currently have the bandwidth to reprex. I can provide an example, but there needs to be at least one FCS file for it to be reproduced:
This produces an error,
The traceback is,
Expected behavior
Because
load_cytoset_from_fcsdoes not specify that the phenoData must have named pData rows, I expect there to be no error.Setting row names for the pData fixes this.
Screenshots
If applicable, add screenshots to help explain your problem.
SessionInfo:
Additional context
Apologies again that I did not fulfil all the requirements for the issue. I thought it best to report the issue in part, rather than give up saying anything about it.