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Cytometry dATa anALYsis Tools
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Error in .check_cd_factor(u$x, u$point_col) : all(y %in% names(colData(x))) is not TRUE #348

Closed denvercal1234GitHub closed 1 year ago

denvercal1234GitHub commented 1 year ago

Hi there,

I ran into an error as above while running clrDR(). Would you mind helping me diagnose this error?

Thank you. 

> names(colData(F37_channelCD3CD8_fcs_data_sce))
[1] "sample_id"                      "cell_count_prePeacoQC"         
[3] "cell_count_postPeacoQC"         "manualInspect_strangeFCS"      
[5] "preFilter_liveCD3CD8_count"     "flowJo_prePeacoQC_gMFI_PE"     
[7] "flowCore_postPeacoQC_medMFI_PE" "cluster_id"           

> CATALYST::clrDR(F37_channelCD3CD8_fcs_data_sce, by = "sample_id", k = "meta25")
Error in .check_cd_factor(u$x, u$point_col) : 
  all(y %in% names(colData(x))) is not TRUE
> session_info()
─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.2.3 (2023-03-15)
 os       macOS Ventura 13.4
 system   aarch64, darwin20
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/London
 date     2023-06-20
 rstudio  2023.06.0+421 Mountain Hydrangea (desktop)
 pandoc   3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)

─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package              * version    date (UTC) lib source
 abind                  1.4-5      2016-07-21 [1] CRAN (R 4.2.0)
 askpass                1.1        2019-01-13 [1] CRAN (R 4.2.0)
 backports              1.4.1      2021-12-13 [1] CRAN (R 4.2.0)
 beachmat               2.14.2     2023-04-09 [1] Bioconductor
 beeswarm               0.4.0      2021-06-01 [1] CRAN (R 4.2.0)
 bigassertr             0.1.6      2023-01-10 [1] CRAN (R 4.2.0)
 bigutilsr              0.3.4      2021-04-13 [1] CRAN (R 4.2.0)
 Biobase              * 2.58.0     2022-11-07 [1] Bioconductor
 BiocGenerics         * 0.44.0     2022-11-07 [1] Bioconductor
 BiocManager            1.30.21    2023-06-10 [1] CRAN (R 4.2.0)
 BiocNeighbors          1.16.0     2022-11-07 [1] Bioconductor
 BiocParallel         * 1.32.6     2023-03-19 [1] Bioconductor
 BiocSingular           1.14.0     2022-11-07 [1] Bioconductor
 bitops                 1.0-7      2021-04-24 [1] CRAN (R 4.2.0)
 bluster              * 1.8.0      2022-11-07 [1] Bioconductor
 broom                  1.0.5      2023-06-09 [1] CRAN (R 4.2.0)
 cachem                 1.0.8      2023-05-01 [1] CRAN (R 4.2.3)
 callr                  3.7.3      2022-11-02 [1] CRAN (R 4.2.0)
 car                    3.1-2      2023-03-30 [1] CRAN (R 4.2.0)
 carData                3.0-5      2022-01-06 [1] CRAN (R 4.2.0)
 caret                * 6.0-94     2023-03-21 [1] CRAN (R 4.2.0)
 CATALYST             * 1.22.0     2022-11-07 [1] Bioconductor
 circlize               0.4.15     2022-05-10 [1] CRAN (R 4.2.0)
 class                * 7.3-22     2023-05-03 [1] CRAN (R 4.2.3)
 cli                    3.6.1      2023-03-23 [1] CRAN (R 4.2.0)
 clue                   0.3-64     2023-01-31 [1] CRAN (R 4.2.0)
 cluster                2.1.4      2022-08-22 [1] CRAN (R 4.2.3)
 codetools              0.2-19     2023-02-01 [1] CRAN (R 4.2.3)
 colorRamps           * 2.3.1      2022-05-02 [1] CRAN (R 4.2.0)
 colorspace             2.1-0      2023-01-23 [1] CRAN (R 4.2.0)
 ComplexHeatmap         2.15.4     2023-05-04 [1] Github (jokergoo/ComplexHeatmap@ae0ec42)
 ConsensusClusterPlus   1.62.0     2022-11-07 [1] Bioconductor
 corpcor                1.6.10     2021-09-16 [1] CRAN (R 4.2.0)
 cowplot                1.1.1      2020-12-30 [1] CRAN (R 4.2.0)
 crayon                 1.5.2      2022-09-29 [1] CRAN (R 4.2.0)
 crul                   1.4.0      2023-05-17 [1] CRAN (R 4.2.3)
 cubature               2.1.0      2023-06-11 [1] CRAN (R 4.2.0)
 curl                   5.0.1      2023-06-07 [1] CRAN (R 4.2.0)
 cytolib                2.10.1     2023-01-23 [1] Bioconductor
 data.table           * 1.14.8     2023-02-17 [1] CRAN (R 4.2.0)
 DBI                    1.1.3      2022-06-18 [1] CRAN (R 4.2.0)
 DelayedArray           0.24.0     2022-11-07 [1] Bioconductor
 DelayedMatrixStats     1.20.0     2022-12-04 [1] Bioconductor
 deldir                 1.0-9      2023-05-17 [1] CRAN (R 4.2.3)
 dendextend             1.17.1     2023-03-25 [1] CRAN (R 4.2.0)
 DEoptimR               1.0-14     2023-06-09 [1] CRAN (R 4.2.0)
 deSolve                1.35       2023-03-12 [1] CRAN (R 4.2.0)
 devtools             * 2.4.5      2022-10-11 [1] CRAN (R 4.2.0)
 digest                 0.6.31     2022-12-11 [1] CRAN (R 4.2.0)
 doParallel             1.0.17     2022-02-07 [1] CRAN (R 4.2.0)
 dplyr                * 1.1.2      2023-04-20 [1] CRAN (R 4.2.0)
 drc                    3.0-1      2016-08-30 [1] CRAN (R 4.2.0)
 DT                     0.28       2023-05-18 [1] CRAN (R 4.2.3)
 ellipsis               0.3.2      2021-04-29 [1] CRAN (R 4.2.0)
 evaluate               0.21       2023-05-05 [1] CRAN (R 4.2.0)
 evd                    2.3-6.1    2022-07-04 [1] CRAN (R 4.2.0)
 evmix                  2.12       2019-09-03 [1] CRAN (R 4.2.0)
 extrafont              0.19       2023-01-18 [1] CRAN (R 4.2.0)
 extrafontdb            1.0        2012-06-11 [1] CRAN (R 4.2.0)
 fansi                  1.0.4      2023-01-22 [1] CRAN (R 4.2.0)
 farver                 2.1.1      2022-07-06 [1] CRAN (R 4.2.0)
 fastmap                1.1.1      2023-02-24 [1] CRAN (R 4.2.0)
 fda                    6.1.4      2023-05-23 [1] CRAN (R 4.2.0)
 fds                    1.8        2018-10-31 [1] CRAN (R 4.2.0)
 fitdistrplus           1.1-11     2023-04-25 [1] CRAN (R 4.2.0)
 flowClust              3.36.1     2023-03-26 [1] Bioconductor
 flowCore             * 2.10.0     2022-11-07 [1] Bioconductor
 FlowSOM              * 2.6.0      2022-11-07 [1] Bioconductor
 flowSpecs              1.12.0     2022-11-07 [1] Bioconductor
 flowStats              4.10.0     2022-11-07 [1] Bioconductor
 flowViz              * 1.62.0     2022-11-07 [1] Bioconductor
 flowVS                 1.30.0     2022-11-07 [1] Bioconductor
 flowWorkspace          4.10.1     2023-01-01 [1] Bioconductor
 fontBitstreamVera      0.1.1      2017-02-01 [1] CRAN (R 4.2.0)
 fontLiberation         0.1.0      2016-10-15 [1] CRAN (R 4.2.0)
 fontquiver             0.2.1      2017-02-01 [1] CRAN (R 4.2.0)
 foreach                1.5.2      2022-02-02 [1] CRAN (R 4.2.0)
 fs                     1.6.2      2023-04-25 [1] CRAN (R 4.2.0)
 future                 1.32.0     2023-03-07 [1] CRAN (R 4.2.0)
 future.apply           1.11.0     2023-05-21 [1] CRAN (R 4.2.3)
 gdtools                0.3.3      2023-03-27 [1] CRAN (R 4.2.0)
 generics               0.1.3      2022-07-05 [1] CRAN (R 4.2.0)
 GenomeInfoDb         * 1.34.9     2023-02-05 [1] Bioconductor
 GenomeInfoDbData       1.2.9      2023-04-24 [1] Bioconductor
 GenomicRanges        * 1.50.2     2022-12-18 [1] Bioconductor
 GetoptLong             1.0.5      2020-12-15 [1] CRAN (R 4.2.0)
 gfonts                 0.2.0      2023-01-08 [1] CRAN (R 4.2.0)
 ggalluvial             0.12.5     2023-02-22 [1] CRAN (R 4.2.0)
 ggbeeswarm             0.7.2      2023-04-29 [1] CRAN (R 4.2.0)
 ggcyto                 1.26.4     2022-12-14 [1] Bioconductor
 ggforce                0.4.1      2022-10-04 [1] CRAN (R 4.2.0)
 ggnewscale             0.4.9      2023-05-25 [1] CRAN (R 4.2.0)
 ggplot2              * 3.4.2      2023-04-03 [1] CRAN (R 4.2.0)
 ggpointdensity       * 0.1.0      2019-08-28 [1] CRAN (R 4.2.0)
 ggpubr               * 0.6.0      2023-02-10 [1] CRAN (R 4.2.0)
 ggraph                 2.1.0      2022-10-09 [1] CRAN (R 4.2.0)
 ggrepel                0.9.3      2023-02-03 [1] CRAN (R 4.2.0)
 ggridges               0.5.4      2022-09-26 [1] CRAN (R 4.2.0)
 ggsignif               0.6.4      2022-10-13 [1] CRAN (R 4.2.0)
 ggthemes             * 4.2.4      2021-01-20 [1] CRAN (R 4.2.0)
 ggVennDiagram          1.2.2      2022-09-08 [1] CRAN (R 4.2.0)
 GlobalOptions          0.1.2      2020-06-10 [1] CRAN (R 4.2.0)
 globals                0.16.2     2022-11-21 [1] CRAN (R 4.2.0)
 glue                   1.6.2      2022-02-24 [1] CRAN (R 4.2.0)
 goftest                1.2-3      2021-10-07 [1] CRAN (R 4.2.0)
 gower                  1.0.1      2022-12-22 [1] CRAN (R 4.2.0)
 graph                  1.76.0     2022-11-07 [1] Bioconductor
 graphlayouts           1.0.0      2023-05-01 [1] CRAN (R 4.2.0)
 gridExtra            * 2.3        2017-09-09 [1] CRAN (R 4.2.0)
 gsl                    2.1-8      2023-01-24 [1] CRAN (R 4.2.0)
 gtable                 0.3.3      2023-03-21 [1] CRAN (R 4.2.0)
 gtools                 3.9.4      2022-11-27 [1] CRAN (R 4.2.0)
 hardhat                1.3.0      2023-03-30 [1] CRAN (R 4.2.0)
 hdrcde                 3.4        2021-01-18 [1] CRAN (R 4.2.0)
 hexbin                 1.28.3     2023-03-21 [1] CRAN (R 4.2.0)
 hrbrthemes             0.8.0      2020-03-06 [1] CRAN (R 4.2.0)
 htmltools              0.5.5      2023-03-23 [1] CRAN (R 4.2.0)
 htmlwidgets            1.6.2      2023-03-17 [1] CRAN (R 4.2.0)
 httpcode               0.3.0      2020-04-10 [1] CRAN (R 4.2.0)
 httpuv                 1.6.11     2023-05-11 [1] CRAN (R 4.2.0)
 httr                   1.4.6      2023-05-08 [1] CRAN (R 4.2.0)
 ica                    1.0-3      2022-07-08 [1] CRAN (R 4.2.0)
 IDPmisc                1.1.20     2020-01-21 [1] CRAN (R 4.2.0)
 igraph               * 1.5.0      2023-06-16 [1] CRAN (R 4.2.3)
 interp                 1.1-4      2023-03-31 [1] CRAN (R 4.2.0)
 ipred                  0.9-14     2023-03-09 [1] CRAN (R 4.2.0)
 IRanges              * 2.32.0     2022-11-07 [1] Bioconductor
 irlba                  2.3.5.1    2022-10-03 [1] CRAN (R 4.2.0)
 iterators              1.0.14     2022-02-05 [1] CRAN (R 4.2.0)
 jpeg                   0.1-10     2022-11-29 [1] CRAN (R 4.2.0)
 jsonlite               1.8.5      2023-06-05 [1] CRAN (R 4.2.0)
 KernSmooth             2.23-21    2023-05-03 [1] CRAN (R 4.2.3)
 knitr                  1.43       2023-05-25 [1] CRAN (R 4.2.0)
 ks                     1.14.0     2022-11-24 [1] CRAN (R 4.2.0)
 labeling               0.4.2      2020-10-20 [1] CRAN (R 4.2.0)
 later                  1.3.1      2023-05-02 [1] CRAN (R 4.2.0)
 lattice              * 0.21-8     2023-04-05 [1] CRAN (R 4.2.0)
 latticeExtra           0.6-30     2022-07-04 [1] CRAN (R 4.2.0)
 lava                   1.7.2.1    2023-02-27 [1] CRAN (R 4.2.0)
 lazyeval               0.2.2      2019-03-15 [1] CRAN (R 4.2.0)
 leiden                 0.4.3      2022-09-10 [1] CRAN (R 4.2.0)
 lifecycle              1.0.3      2022-10-07 [1] CRAN (R 4.2.0)
 listenv                0.9.0      2022-12-16 [1] CRAN (R 4.2.0)
 lmtest                 0.9-40     2022-03-21 [1] CRAN (R 4.2.0)
 lubridate              1.9.2      2023-02-10 [1] CRAN (R 4.2.0)
 magrittr               2.0.3      2022-03-30 [1] CRAN (R 4.2.0)
 MASS                   7.3-60     2023-05-04 [1] CRAN (R 4.2.3)
 Matrix                 1.5-4.1    2023-05-18 [1] CRAN (R 4.2.3)
 MatrixGenerics       * 1.10.0     2022-11-07 [1] Bioconductor
 matrixStats          * 1.0.0      2023-06-02 [1] CRAN (R 4.2.0)
 mclust                 6.0.0      2022-10-31 [1] CRAN (R 4.2.0)
 memoise                2.0.1      2021-11-26 [1] CRAN (R 4.2.0)
 mgcv                   1.8-42     2023-03-02 [1] CRAN (R 4.2.3)
 mime                   0.12       2021-09-28 [1] CRAN (R 4.2.0)
 miniUI                 0.1.1.1    2018-05-18 [1] CRAN (R 4.2.0)
 mnormt                 2.1.1      2022-09-26 [1] CRAN (R 4.2.0)
 ModelMetrics           1.2.2.2    2020-03-17 [1] CRAN (R 4.2.0)
 multcomp               1.4-24     2023-06-14 [1] CRAN (R 4.2.0)
 munsell                0.5.0      2018-06-12 [1] CRAN (R 4.2.0)
 mvtnorm                1.2-2      2023-06-08 [1] CRAN (R 4.2.0)
 ncdfFlow               2.44.0     2022-11-07 [1] Bioconductor
 nlme                   3.1-162    2023-01-31 [1] CRAN (R 4.2.3)
 nnet                   7.3-19     2023-05-03 [1] CRAN (R 4.2.3)
 nnls                   1.4        2012-03-19 [1] CRAN (R 4.2.0)
 openCyto               2.10.1     2022-12-02 [1] Bioconductor
 openssl                2.0.6      2023-03-09 [1] CRAN (R 4.2.0)
 parallelly             1.36.0     2023-05-26 [1] CRAN (R 4.2.0)
 patchwork              1.1.2      2022-08-19 [1] CRAN (R 4.2.0)
 pbapply                1.7-0      2023-01-13 [1] CRAN (R 4.2.0)
 pcaPP                  2.0-3      2022-10-24 [1] CRAN (R 4.2.0)
 PeacoQC                1.9.3      2023-04-20 [1] Github (saeyslab/PeacoQC@64c84ad)
 permute                0.9-7      2022-01-27 [1] CRAN (R 4.2.0)
 pheatmap             * 1.0.12     2019-01-04 [1] CRAN (R 4.2.0)
 pillar                 1.9.0      2023-03-22 [1] CRAN (R 4.2.0)
 pkgbuild               1.4.1      2023-06-14 [1] CRAN (R 4.2.3)
 pkgconfig              2.0.3      2019-09-22 [1] CRAN (R 4.2.0)
 pkgload                1.3.2      2022-11-16 [1] CRAN (R 4.2.0)
 plotly                 4.10.2     2023-06-03 [1] CRAN (R 4.2.0)
 plotrix                3.8-2      2021-09-08 [1] CRAN (R 4.2.0)
 plyr                 * 1.8.8      2022-11-11 [1] CRAN (R 4.2.0)
 png                    0.1-8      2022-11-29 [1] CRAN (R 4.2.0)
 polyclip               1.10-4     2022-10-20 [1] CRAN (R 4.2.0)
 powerTCR               1.18.0     2022-11-07 [1] Bioconductor
 pracma                 2.4.2      2022-09-22 [1] CRAN (R 4.2.0)
 prettyunits            1.1.1      2020-01-24 [1] CRAN (R 4.2.0)
 pROC                   1.18.2     2023-05-13 [1] CRAN (R 4.2.0)
 processx               3.8.1      2023-04-18 [1] CRAN (R 4.2.0)
 prodlim                2023.03.31 2023-04-02 [1] CRAN (R 4.2.0)
 profvis                0.3.8      2023-05-02 [1] CRAN (R 4.2.0)
 progressr              0.13.0     2023-01-10 [1] CRAN (R 4.2.0)
 promises               1.2.0.1    2021-02-11 [1] CRAN (R 4.2.0)
 ps                     1.7.5      2023-04-18 [1] CRAN (R 4.2.0)
 purrr                  1.0.1      2023-01-10 [1] CRAN (R 4.2.0)
 R6                     2.5.1      2021-08-19 [1] CRAN (R 4.2.0)
 rainbow                3.7        2022-10-09 [1] CRAN (R 4.2.0)
 RANN                   2.6.1      2019-01-08 [1] CRAN (R 4.2.0)
 RBGL                   1.74.0     2022-11-07 [1] Bioconductor
 RColorBrewer         * 1.1-3      2022-04-03 [1] CRAN (R 4.2.0)
 Rcpp                   1.0.10     2023-01-22 [1] CRAN (R 4.2.0)
 RcppAnnoy              0.0.20     2022-10-27 [1] CRAN (R 4.2.0)
 RCurl                  1.98-1.12  2023-03-27 [1] CRAN (R 4.2.0)
 recipes                1.0.6      2023-04-25 [1] CRAN (R 4.2.3)
 remotes                2.4.2      2021-11-30 [1] CRAN (R 4.2.0)
 reshape2               1.4.4      2020-04-09 [1] CRAN (R 4.2.0)
 reticulate           * 1.30       2023-06-09 [1] CRAN (R 4.2.0)
 rgdal                  1.6-7      2023-05-31 [1] CRAN (R 4.2.0)
 rgeos                  0.6-3      2023-05-24 [1] CRAN (R 4.2.0)
 Rgraphviz              2.42.0     2022-11-07 [1] Bioconductor
 rjson                  0.2.21     2022-01-09 [1] CRAN (R 4.2.0)
 rlang                  1.1.1      2023-04-28 [1] CRAN (R 4.2.0)
 rmarkdown              2.22       2023-06-01 [1] CRAN (R 4.2.0)
 robustbase             0.99-0     2023-06-16 [1] CRAN (R 4.2.3)
 ROCR                   1.0-11     2020-05-02 [1] CRAN (R 4.2.0)
 rpart                  4.1.19     2022-10-21 [1] CRAN (R 4.2.3)
 Rphenograph          * 0.99.1     2023-05-19 [1] Github (JinmiaoChenLab/Rphenograph@0298487)
 RProtoBufLib           2.10.0     2022-11-07 [1] Bioconductor
 rrcov                  1.7-3      2023-05-17 [1] CRAN (R 4.2.3)
 RSpectra               0.16-1     2022-04-24 [1] CRAN (R 4.2.0)
 rstatix                0.7.2      2023-02-01 [1] CRAN (R 4.2.0)
 rstudioapi           * 0.14       2022-08-22 [1] CRAN (R 4.2.0)
 rsvd                   1.0.5      2021-04-16 [1] CRAN (R 4.2.0)
 Rtsne                * 0.16       2022-04-17 [1] CRAN (R 4.2.0)
 Rttf2pt1               1.3.12     2023-01-22 [1] CRAN (R 4.2.0)
 RVenn                  1.1.0      2019-07-18 [1] CRAN (R 4.2.0)
 S4Vectors            * 0.36.2     2023-03-01 [1] Bioconductor
 sandwich               3.0-2      2022-06-15 [1] CRAN (R 4.2.0)
 ScaledMatrix           1.6.0      2022-11-07 [1] Bioconductor
 scales               * 1.2.1      2022-08-20 [1] CRAN (R 4.2.0)
 scater                 1.26.1     2022-11-13 [1] Bioconductor
 scattermore            1.2        2023-06-12 [1] CRAN (R 4.2.0)
 scRepertoire           1.8.0      2022-11-07 [1] Bioconductor
 sctransform            0.3.5      2022-09-21 [1] CRAN (R 4.2.0)
 scuttle                1.8.4      2023-01-22 [1] Bioconductor
 sessioninfo            1.2.2      2021-12-06 [1] CRAN (R 4.2.0)
 Seurat                 4.3.0      2022-11-18 [1] CRAN (R 4.2.0)
 SeuratObject           4.1.3      2022-11-07 [1] CRAN (R 4.2.0)
 shape                  1.4.6      2021-05-19 [1] CRAN (R 4.2.0)
 shiny                  1.7.4      2022-12-15 [1] CRAN (R 4.2.0)
 SingleCellExperiment * 1.20.1     2023-03-19 [1] Bioconductor
 sp                     1.6-1      2023-05-31 [1] CRAN (R 4.2.0)
 SparseM                1.81       2021-02-18 [1] CRAN (R 4.2.0)
 sparseMatrixStats      1.10.0     2022-11-07 [1] Bioconductor
 spatstat.data          3.0-1      2023-03-12 [1] CRAN (R 4.2.0)
 spatstat.explore       3.2-1      2023-05-13 [1] CRAN (R 4.2.0)
 spatstat.geom          3.2-1      2023-05-09 [1] CRAN (R 4.2.0)
 spatstat.random        3.1-5      2023-05-11 [1] CRAN (R 4.2.0)
 spatstat.sparse        3.0-1      2023-03-12 [1] CRAN (R 4.2.0)
 spatstat.utils         3.0-3      2023-05-09 [1] CRAN (R 4.2.0)
 Spectre              * 1.0.0      2023-04-20 [1] Github (immunedynamics/spectre@3d0c002)
 stringdist             0.9.10     2022-11-07 [1] CRAN (R 4.2.0)
 stringi                1.7.12     2023-01-11 [1] CRAN (R 4.2.0)
 stringr                1.5.0      2022-12-02 [1] CRAN (R 4.2.0)
 SummarizedExperiment * 1.28.0     2022-11-07 [1] Bioconductor
 survival               3.5-5      2023-03-12 [1] CRAN (R 4.2.0)
 systemfonts            1.0.4      2022-02-11 [1] CRAN (R 4.2.0)
 tensor                 1.5        2012-05-05 [1] CRAN (R 4.2.0)
 TH.data                1.1-2      2023-04-17 [1] CRAN (R 4.2.0)
 tibble                 3.2.1      2023-03-20 [1] CRAN (R 4.2.0)
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 [1] /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
HelenaLC commented 1 year ago

Having a look at ?clrDR, you can see that for by = "sample_id", point_col defaults to "condition", i.e., points will be colored by the sample of origin's experimental condition. However, you're data doesn't contain a condition cell metadata slot. If you altered the defaults in prepData, you need to also adjust the parameters in downstream visualization functions. E.g., here, point_col needs to be a valid colData variable.