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rowData(F37_channelCD3CD8_fcs_data_sce)$marker_class returned all "none" #347

Closed denvercal1234GitHub closed 1 year ago

denvercal1234GitHub commented 1 year ago

Hi there,

Thanks for the tool.

I did the following but when I checked rowData(F37_channelCD3CD8_fcs_data_sce)$marker_class, all were "none" with Levels being still "type", "state", and "none."

And, cluster returned Error in .get_features(x, features) : No features matched the specified marker class.

Would you mind letting me know how to proceed?

F37_channelCD3CD8_fcs_data_sce <- prepData(x=F37_channelCD3CD8_fcs_data, transformation = F, truncate_max_range=F,FACS=T, panel=F37_channelCD3CD8_fcs_data_panel, md=filtered_meta_F37_CD4CD8DP_Untransformed_TRIAL_fcs_data_RemovedMargin_sample.info, 
    panel_cols = list(channel = "F37_channelCD3CD8_fcs_data_fcs_colname", antigen = "F37_channelCD3CD8_fcs_data_antigen", factors =  c("F37_channelCD3CD8_fcs_data_marker_class")),
    md_cols = list(file = "channelFCS_file_name", id = "file_name", 
        factors = c("cell_count_prePeacoQC", "cell_count_postPeacoQC", "manualInspect_strangeFCS", "preFilter_liveCD3CD8_count", "flowJo_prePeacoQC_gMFI_PE", "flowCore_postPeacoQC_medMFI_PE")))
> rowData(F37_channelCD3CD8_fcs_data_sce)$marker_class
  [1] none none none none none none none none none none none none none none none none
 [17] none none none none none none none none none none none none none none none none
 [33] none none none none none none none none none none none none none none none none
 [49] none none none none none none none none none none none none none none none none
 [65] none none none none none none none none none none none none none none none none
 [81] none none none none none none none none none none none none none none none none
 [97] none none none none none none none none none none none none none none none none
[113] none none none none none none none none none none none none none none none none
[129] none none none none none none none none none none none none none none none none
[145] none none none none none none none none none none none none none none none none
[161] none none none none none none none none none none none none none none none none
[177] none none none none none none none none none none none none none none none none
[193] none none none none none none none none none none none none none none none none
[209] none none none none none none none none none none none none none none none none
[225] none none none none none none none none none none none none none none none none
[241] none none none none none none none none none none none none none none none none
[257] none none none none none none none none none none none none none none
Levels: type state none

Related = #84 #335 

> 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)
 AnnotationDbi        * 1.60.2      2023-03-12 [1] Bioconductor
 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)
 base64enc              0.1-3       2015-07-28 [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)
 BH                   * 1.81.0-1    2023-01-22 [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
 Biostrings           * 2.66.0      2022-11-07 [1] Bioconductor
 bit                    4.0.5       2022-11-15 [1] CRAN (R 4.2.0)
 bit64                  4.0.5       2020-08-30 [1] CRAN (R 4.2.0)
 bitops                 1.0-7       2021-04-24 [1] CRAN (R 4.2.0)
 blob                   1.2.4       2023-03-17 [1] CRAN (R 4.2.0)
 broom                  1.0.5       2023-06-09 [1] CRAN (R 4.2.0)
 bslib                  0.5.0       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
 changepoint            2.2.4       2022-11-03 [1] CRAN (R 4.2.0)
 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
 ConsRank             * 2.1.3       2023-03-23 [1] CRAN (R 4.2.0)
 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
 CytoNorm             * 0.0.15      2023-04-25 [1] Github (saeyslab/CytoNorm@78c6675)
 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
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 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)
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 doParallel             1.0.17      2022-02-07 [1] CRAN (R 4.2.0)
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 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)
 factoextra           * 1.0.7       2020-04-01 [1] CRAN (R 4.2.0)
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 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)
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 flowAssist           * 0.0.0.9000  2023-04-25 [1] Github (ssmpsn2/flowAssist@3910e63)
 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
 flowTrans            * 1.50.0      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)
 hms                    1.1.3       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)
 janitor              * 2.2.0       2023-02-02 [1] CRAN (R 4.2.0)
 jpeg                   0.1-10      2022-11-29 [1] CRAN (R 4.2.0)
 jquerylib              0.1.4       2021-04-26 [1] CRAN (R 4.2.0)
 jsonlite               1.8.5       2023-06-05 [1] CRAN (R 4.2.0)
 KEGGREST               1.38.0      2022-11-07 [1] Bioconductor
 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)
 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)
 modeltools           * 0.2-23      2020-03-05 [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)
 NbClust              * 3.0.1       2022-05-02 [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)
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 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)
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 pkgload                1.3.2       2022-11-16 [1] CRAN (R 4.2.0)
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 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)
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 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)
 randomcoloR          * 1.1.0.1     2019-11-24 [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)
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 rgl                  * 1.1.3       2023-03-26 [1] CRAN (R 4.2.0)
 Rgraphviz              2.42.0      2022-11-07 [1] Bioconductor
 rJava                  1.0-6       2021-12-10 [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
  1. In prepData, argument panel_cols defaults to having a marker_class column in the panel that contains marker classes (type, state, none). In your example, this doesn't exist. Consequently, all markers are assigned a class of none.
  2. cluster in turn defaults to using marker of class type, but there aren't any, hence the error. So there are 3 solutions: either 1) specify marker classes in the input panel in prepData, and set the corresponding column in panel_cols (preferred), or 2) set marker classes after the SCE has been constructed via rowData(sce)$marker_class <- ... or 3) pass the markers to use directly to cluster's features argument. 1) Is best here because many of CATALYST's functions default to using type or state markers (it depends), and if these aren't set you'll have to always pass them manually to a given function...