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DillonHammill / CytoExploreR

Interactive Cytometry Data Analysis
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cyto_gate_draw() error: subset out of bounds #142

Open GKok opened 2 years ago

GKok commented 2 years ago

Hi Dillon,

I've started using your package(s) again to analyse new data. I'm re-using a script from last year, which worked well, but with updated versions of all packages.

When drawing gates, I'm running into an unspecified problem. I can't find a solution online or here, on Github. Would you know what's going wrong?

My code:

library("flowCore")
library("flowWorkspace")
library("openCyto")
library("CytoExploreR")
library("dplyr")

path <- "20220405_FACS/"

setwd(path)

# Load files
fcs <- load_cytoset_from_fcs(path = path, 
                             transformation = FALSE, 
                             alter.names = TRUE, 
                             sep = "\t",
                             phenoData = "samples.tsv"
)

#Check markers
cyto_markers(fcs)
cyto_details(fcs)

# Create gating set
gs <- GatingSet(fcs)

# Display sample names
sampleNames <- cyto_names(gs)
write.csv(sampleNames, "sampleNames.csv", row.names = FALSE)

# Fluorescent channels (display + select)
chans <- cyto_fluor_channels(gs)
chans
usedChans <- c("FL1-A",  #GFP
               "FL6-A",  #DAPI
               "FL11-A") #RFP

# All channels (display)
cyto_channels(gs)

# Log transformation
gs <- cyto_transform(gs, 
                     channels = usedChans, 
                     type="biex", 
                     plot=TRUE,
                     axes_limits="machine",
                     maxValue=16777215)

# Create empty gatingTemplate
cyto_gatingTemplate_create("gates.csv")
# Select new gatingTemplate as active
cyto_gatingTemplate_select("gates.csv")

# Draw gates
# Cells
cyto_gate_draw(gs,
               select=list(name="A1.fcs"),
               parent = "root",
               alias = "Cells",
               channels = c("FSC-A","SSC-A"),
               type = "polygon",
               xlim = c(0,6000000),
               ylim = c(0,8000000),
               gatingTemplate = "gates.csv")

The error:

> cyto_gate_draw(gs,
+                select=list(name="A1.fcs"),
+                parent = "root",
+                alias = "Cells",
+                channels = c("FSC-A","SSC-A"),
+                type = "polygon",
+                xlim = c(0,6000000),
+                ylim = c(0,8000000),
+                gatingTemplate = "gates.csv")
Error: Subset out of bounds
> traceback()
10: stop("Subset out of bounds", call. = FALSE)
9: x[ind]
8: x[ind]
7: FUN(X[[i]], ...)
6: lapply(seq_len(length(pd_split)), function(z) {
       ind <- match(pd_split[[z]][, "name"], cyto_names(x))
       x[ind]
   })
5: cyto_group_by(x, group_by = merge_by)
4: cyto_merge_by.flowSet(fs, merge_by = group_by, select = select)
3: cyto_merge_by(fs, merge_by = group_by, select = select)
2: cyto_gate_draw.GatingSet(gs, select = list(name = "A1.fcs"), parent = "root", 
       alias = "Cells", channels = c("FSC-A", "SSC-A"), type = "polygon", 
       xlim = c(0, 6000000), ylim = c(0, 8000000), gatingTemplate = "gates.csv")
1: cyto_gate_draw(gs, select = list(name = "A1.fcs"), parent = "root", 
       alias = "Cells", channels = c("FSC-A", "SSC-A"), type = "polygon", 
       xlim = c(0, 6000000), ylim = c(0, 8000000), gatingTemplate = "gates.csv")

Not sure if it helps, but the first lines of cyto_details:

> head(cyto_details(gs))
     name varX varY       date varZ donor gene
A1 A1.fcs        100    100 05-04-2022        K0 xxx none
A2 A2.fcs          0    100 05-04-2022        K0 xxx none
A3 A3.fcs        100      1 05-04-2022        K0 xxx none
A4 A4.fcs          0      1 05-04-2022        K0 xxx none
A5 A5.fcs        100   1000 05-04-2022        K0 xxx none
A6 A6.fcs          0   1000 05-04-2022        K0 xxx none
> sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 12.3.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] nl_NL.UTF-8/nl_NL.UTF-8/nl_NL.UTF-8/C/nl_NL.UTF-8/nl_NL.UTF-8

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

other attached packages:
 [1] ggridges_0.5.3           dplyr_1.0.8              cytoqc_0.99.2            CytoML_2.7.2             ggcyto_1.18.0           
 [6] ncdfFlow_2.36.0          BH_1.78.0-0              RcppArmadillo_0.11.0.0.0 ggplot2_3.3.5            cytoverse_0.0.0.9000    
[11] CytoExploreR_1.1.0       openCyto_2.5.4           flowWorkspace_4.7.1      flowCore_2.7.1          

loaded via a namespace (and not attached):
  [1] changepoint_2.2.3   systemfonts_1.0.4   plyr_1.8.7          splines_4.0.5       fda_5.5.1           usethis_2.1.5      
  [7] digest_0.6.29       htmltools_0.5.2     fansi_1.0.3         magrittr_2.0.3      memoise_2.0.1       cluster_2.1.3      
 [13] ks_1.13.4           hdrcde_3.4          aws.signature_0.6.0 remotes_2.4.2       RcppParallel_5.1.5  matrixStats_0.61.0 
 [19] R.utils_2.11.0      svglite_2.1.0       askpass_1.1         fds_1.8             cytolib_2.7.4       prettyunits_1.1.1  
 [25] jpeg_0.1-9          colorspace_2.0-3    rvest_1.0.2         rrcov_1.6-2         xfun_0.30           callr_3.7.0        
 [31] crayon_1.5.1        RCurl_1.98-1.6      jsonlite_1.8.0      hexbin_1.28.2       graph_1.68.0        zoo_1.8-9          
 [37] glue_1.6.2          kableExtra_1.3.4    flowClust_3.28.0    gtable_0.3.0        zlibbioc_1.36.0     webshot_0.5.2      
 [43] pkgbuild_1.3.1      IDPmisc_1.1.20      Rgraphviz_2.34.0    BiocGenerics_0.36.1 DEoptimR_1.0-11     scales_1.1.1       
 [49] mvtnorm_1.1-3       DBI_1.1.2           Rcpp_1.0.8.3        viridisLite_0.4.0   xtable_1.8-4        tmvnsim_1.0-2      
 [55] clue_0.3-60         reticulate_1.24     rsvd_1.0.5          mclust_5.4.9        deSolve_1.31        colortable_0.3.0   
 [61] DT_0.22             umap_0.2.8.0        stats4_4.0.5        htmlwidgets_1.5.4   httr_1.4.2          RColorBrewer_1.1-3 
 [67] ellipsis_0.3.2      rainbow_3.6         pkgconfig_2.0.3     XML_3.99-0.9        R.methodsS3_1.8.1   flowViz_1.54.0     
 [73] sass_0.4.1          utf8_1.2.2          flowStats_4.2.0     tidyselect_1.1.2    rlang_1.0.2         reshape2_1.4.4     
 [79] later_1.3.0         visNetwork_2.1.0    munsell_0.5.0       tools_4.0.5         cachem_1.0.6        cli_3.2.0          
 [85] generics_0.1.2      devtools_2.4.3      aws.s3_0.3.21       evaluate_0.15       stringr_1.4.0       fastmap_1.1.0      
 [91] yaml_2.3.5          processx_3.5.3      knitr_1.38          fs_1.5.2            EmbedSOM_2.1.1      robustbase_0.95-0  
 [97] purrr_0.3.4         RBGL_1.66.0         mime_0.12           rhandsontable_0.3.8 R.oo_1.24.0         pracma_2.3.8       
[103] xml2_1.3.3          brio_1.1.3          compiler_4.0.5      rstudioapi_0.13     curl_4.3.2          png_0.1-7          
[109] testthat_3.1.3      tibble_3.1.6        bslib_0.3.1         pcaPP_1.9-74        stringi_1.7.6       ps_1.6.0           
[115] RSpectra_0.16-0     desc_1.4.1          lattice_0.20-45     Matrix_1.4-1        vctrs_0.4.0         pillar_1.7.0       
[121] lifecycle_1.0.1     flowAI_1.20.1       BiocManager_1.30.16 jquerylib_0.1.4     data.table_1.14.2   bitops_1.0-7       
[127] corpcor_1.6.10      httpuv_1.6.5        R6_2.5.1            latticeExtra_0.6-29 promises_1.2.0.1    gridExtra_2.3      
[133] KernSmooth_2.23-20  RProtoBufLib_2.7.4  sessioninfo_1.2.2   MASS_7.3-56         gtools_3.9.2        assertthat_0.2.1   
[139] pkgload_1.2.4       openssl_2.0.0       rprojroot_2.0.3     withr_2.5.0         mnormt_2.0.2        S4Vectors_0.28.1   
[145] parallel_4.0.5      grid_4.0.5          tidyr_1.2.0         rmarkdown_2.13      Rtsne_0.15          Biobase_2.50.0     
[151] shiny_1.7.1         base64enc_0.1-3     ellipse_0.4.2

Thank you,

Gautam

DillonHammill commented 2 years ago

Hmmm... I think it is your selection criteria, can you include the printout of cyto_deatils(gs)?

GKok commented 2 years ago

They're included in my opening post:

> head(cyto_details(gs))
     name varX varY       date varZ donor gene
A1 A1.fcs        100    100 05-04-2022        K0 xxx none
A2 A2.fcs          0    100 05-04-2022        K0 xxx none
A3 A3.fcs        100      1 05-04-2022        K0 xxx none
A4 A4.fcs          0      1 05-04-2022        K0 xxx none
A5 A5.fcs        100   1000 05-04-2022        K0 xxx none
A6 A6.fcs          0   1000 05-04-2022        K0 xxx none
DillonHammill commented 2 years ago

Can you try setting select = 1 instead?

GKok commented 2 years ago

Same error.

> cyto_gate_draw(gs,
+                #select=list(name="A1.fcs"),
+                select=1,
+                parent = "root",
+                alias = "Cells",
+                channels = c("FSC-A","SSC-A"),
+                type = "polygon",
+                xlim = c(0,6000000),
+                ylim = c(0,8000000),
+                gatingTemplate = "gates.csv")
Error: Subset out of bounds
DillonHammill commented 2 years ago

And if you remove select completely does it run?

GKok commented 2 years ago

No, still throws the same error.

DillonHammill commented 2 years ago

Yeah OK it looks like the cyto_names() may be out of sync with the rownames of cyto_details(). I have already fixed this in the new version (coming soon), I can take a look tomorrow to see if I can patch it in the meantime.

GKok commented 2 years ago

Thank you, I really appreciate it.

DillonHammill commented 2 years ago

@GKok I don't want to waste time fixing this for the current version. Perhaps in the meantime you could try running the following before gating:

cyto_details(gs)$name <- rownames(cyto_details(gs))

This should get everything back in sync and the gating should proceed.