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wejlab / animalcules

R shiny app for interactive microbiome analysis
https://wejlab.github.io/animalcules-docs/
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Incorrect options for Select Target Condition in Biomarker Analysis #44

Closed jarrodscott closed 3 years ago

jarrodscott commented 3 years ago

Hello,

This may or may not be an issue but for some reason, in the Biomarker tab under Select Target Condition the only options that appear are SEX and DISEASE, neither of which are in my data set. In every other tab, my specific metadata shows up. I have tried formatting the files as comma and tab separators but the result is the same. I did upload example data and that seems to work just fine. For example, if I choose the Asthma metatranscriptomics data set, the only option is Asthma_status in the Biomarker tab. What's more, if I then go back and try uploading my data again, this time the option is Asthma_status in the Biomarker tab instead of SEX and DISEASE. However, if I go back and forth between the example data sets, the options change accordingly.

Any idea what is causing this or how I can troubleshoot the issue?

Below I include the results of loading the animalcules and then running sessionInfo() and devtools::session_info().

Thank you for your time! Jarrod

Screen Shot 2021-03-12 at 9 33 26 AM 
> library(BiocManager)
Bioconductor version 3.12 (BiocManager 1.30.10), ?BiocManager::install for help
> 
> library(animalcules)
Registered S3 method overwritten by 'quantmod':
  method            from
  as.zoo.data.frame zoo 
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.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] animalcules_1.7.0

loaded via a namespace (and not attached):
  [1] colorspace_2.0-0            ellipsis_0.3.1              class_7.3-18                XVector_0.30.0              GenomicRanges_1.42.0       
  [6] MultiAssayExperiment_1.16.0 DT_0.17                     bit64_4.0.5                 RSpectra_0.16-0             AnnotationDbi_1.52.0       
 [11] prodlim_2019.11.13          fansi_0.4.2                 lubridate_1.7.10            codetools_0.2-18            splines_4.0.3              
 [16] cachem_1.0.4                geneplotter_1.68.0          DMwR_0.4.1                  plotROC_2.2.1               jsonlite_1.7.2             
 [21] pROC_1.17.0.1               umap_0.2.7.0                caret_6.0-86                annotate_1.68.0             cluster_2.1.1              
 [26] rentrez_1.2.3               compiler_4.0.3              httr_1.4.2                  assertthat_0.2.1            Matrix_1.3-2               
 [31] fastmap_1.1.0               lazyeval_0.2.2              limma_3.46.0                htmltools_0.5.1.1           tools_4.0.3                
 [36] gtable_0.3.0                glue_1.4.2                  GenomeInfoDbData_1.2.4      reshape2_1.4.4              dplyr_1.0.5                
 [41] Rcpp_1.0.6                  Biobase_2.50.0              vctrs_0.3.6                 rhdf5filters_1.2.0          debugme_1.1.0              
 [46] ape_5.4-1                   nlme_3.1-152                iterators_1.0.13            timeDate_3043.102           gower_0.2.2                
 [51] stringr_1.4.0               lifecycle_1.0.0             GUniFrac_1.1                XML_3.99-0.5                zlibbioc_1.36.0            
 [56] MASS_7.3-53.1               zoo_1.8-9                   scales_1.1.1                ipred_0.9-10                MatrixGenerics_1.2.1       
 [61] rex_1.2.0                   parallel_4.0.3              SummarizedExperiment_1.20.0 biomformat_1.18.0           rhdf5_2.34.0               
 [66] RColorBrewer_1.1-2          quantmod_0.4.18             curl_4.3                    reticulate_1.18             memoise_2.0.0              
 [71] ggplot2_3.3.3               rpart_4.1-15                stringi_1.5.3               RSQLite_2.2.3               genefilter_1.72.1          
 [76] S4Vectors_0.28.1            foreach_1.5.1               permute_0.9-5               TTR_0.24.2                  BiocGenerics_0.36.0        
 [81] BiocParallel_1.24.1         shape_1.4.5                 lava_1.6.8.1                GenomeInfoDb_1.26.2         rlang_0.4.10               
 [86] pkgconfig_2.0.3             matrixStats_0.58.0          bitops_1.0-6                lattice_0.20-41             ROCR_1.0-11                
 [91] purrr_0.3.4                 Rhdf5lib_1.12.1             recipes_0.1.15              htmlwidgets_1.5.3           bit_4.0.4                  
 [96] tidyselect_1.1.0            plyr_1.8.6                  magrittr_2.0.1              DESeq2_1.30.1               R6_2.5.0                   
[101] IRanges_2.24.1              generics_0.1.0              DelayedArray_0.16.2         DBI_1.1.1                   pillar_1.5.1               
[106] withr_2.4.1                 mgcv_1.8-34                 xts_0.12.1                  survival_3.2-7              abind_1.4-5                
[111] RCurl_1.98-1.2              nnet_7.3-15                 tsne_0.1-3                  tibble_3.1.0                crayon_1.4.1               
[116] utf8_1.1.4                  plotly_4.9.3                locfit_1.5-9.4              grid_4.0.3                  data.table_1.14.0          
[121] blob_1.2.1                  vegan_2.5-7                 forcats_0.5.1               ModelMetrics_1.2.2.2        digest_0.6.27              
[126] xtable_1.8-4                tidyr_1.1.3                 covr_3.5.1                  openssl_1.4.3               glmnet_4.1-1               
[131] stats4_4.0.3                munsell_0.5.0               viridisLite_0.3.0           shinyjs_2.0.0               askpass_1.1                
> devtools::session_info()
─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.0.3 (2020-10-10)
 os       macOS Catalina 10.15.7      
 system   x86_64, darwin17.0          
 ui       AQUA                        
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       America/Panama              
 date     2021-03-12                  

─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package              * version    date       lib source                                 
 abind                  1.4-5      2016-07-21 [1] CRAN (R 4.0.0)                         
 animalcules          * 1.7.0      2021-03-10 [1] Github (compbiomed/animalcules@59b3361)
 annotate               1.68.0     2020-10-27 [1] Bioconductor                           
 AnnotationDbi          1.52.0     2020-10-27 [1] Bioconductor                           
 ape                    5.4-1      2020-08-13 [1] CRAN (R 4.0.2)                         
 askpass                1.1        2019-01-13 [1] CRAN (R 4.0.0)                         
 assertthat             0.2.1      2019-03-21 [1] CRAN (R 4.0.0)                         
 Biobase                2.50.0     2020-10-27 [1] Bioconductor                           
 BiocGenerics           0.36.0     2020-10-27 [1] Bioconductor                           
 BiocParallel           1.24.1     2020-11-06 [1] Bioconductor                           
 biomformat             1.18.0     2020-10-27 [1] Bioconductor                           
 bit                    4.0.4      2020-08-04 [1] CRAN (R 4.0.2)                         
 bit64                  4.0.5      2020-08-30 [1] CRAN (R 4.0.2)                         
 bitops                 1.0-6      2013-08-17 [1] CRAN (R 4.0.0)                         
 blob                   1.2.1      2020-01-20 [1] CRAN (R 4.0.0)                         
 cachem                 1.0.4      2021-02-13 [1] CRAN (R 4.0.2)                         
 callr                  3.5.1      2020-10-13 [1] CRAN (R 4.0.2)                         
 caret                  6.0-86     2020-03-20 [1] CRAN (R 4.0.0)                         
 class                  7.3-18     2021-01-24 [1] CRAN (R 4.0.2)                         
 cli                    2.3.1      2021-02-23 [1] CRAN (R 4.0.2)                         
 cluster                2.1.1      2021-02-14 [1] CRAN (R 4.0.2)                         
 codetools              0.2-18     2020-11-04 [1] CRAN (R 4.0.2)                         
 colorspace             2.0-0      2020-11-11 [1] CRAN (R 4.0.2)                         
 covr                   3.5.1      2020-09-16 [1] CRAN (R 4.0.2)                         
 crayon                 1.4.1      2021-02-08 [1] CRAN (R 4.0.2)                         
 curl                   4.3        2019-12-02 [1] CRAN (R 4.0.0)                         
 data.table             1.14.0     2021-02-21 [1] CRAN (R 4.0.2)                         
 DBI                    1.1.1      2021-01-15 [1] CRAN (R 4.0.2)                         
 debugme                1.1.0      2017-10-22 [1] CRAN (R 4.0.2)                         
 DelayedArray           0.16.2     2021-02-26 [1] Bioconductor                           
 desc                   1.3.0      2021-03-05 [1] CRAN (R 4.0.2)                         
 DESeq2                 1.30.1     2021-02-19 [1] Bioconductor                           
 devtools               2.3.2      2020-09-18 [1] CRAN (R 4.0.2)                         
 digest                 0.6.27     2020-10-24 [1] CRAN (R 4.0.2)                         
 DMwR                   0.4.1      2013-08-08 [1] CRAN (R 4.0.0)                         
 dplyr                  1.0.5      2021-03-05 [1] CRAN (R 4.0.2)                         
 DT                     0.17       2021-01-06 [1] CRAN (R 4.0.2)                         
 ellipsis               0.3.1      2020-05-15 [1] CRAN (R 4.0.0)                         
 fansi                  0.4.2      2021-01-15 [1] CRAN (R 4.0.2)                         
 fastmap                1.1.0      2021-01-25 [1] CRAN (R 4.0.2)                         
 forcats                0.5.1      2021-01-27 [1] CRAN (R 4.0.2)                         
 foreach                1.5.1      2020-10-15 [1] CRAN (R 4.0.2)                         
 fs                     1.5.0      2020-07-31 [1] CRAN (R 4.0.2)                         
 genefilter             1.72.1     2021-01-21 [1] Bioconductor                           
 geneplotter            1.68.0     2020-10-27 [1] Bioconductor                           
 generics               0.1.0      2020-10-31 [1] CRAN (R 4.0.2)                         
 GenomeInfoDb           1.26.2     2020-12-08 [1] Bioconductor                           
 GenomeInfoDbData       1.2.4      2021-01-25 [1] Bioconductor                           
 GenomicRanges          1.42.0     2020-10-27 [1] Bioconductor                           
 ggplot2                3.3.3      2020-12-30 [1] CRAN (R 4.0.2)                         
 glmnet                 4.1-1      2021-02-21 [1] CRAN (R 4.0.2)                         
 glue                   1.4.2      2020-08-27 [1] CRAN (R 4.0.2)                         
 gower                  0.2.2      2020-06-23 [1] CRAN (R 4.0.0)                         
 gtable                 0.3.0      2019-03-25 [1] CRAN (R 4.0.0)                         
 GUniFrac               1.1        2018-02-12 [1] CRAN (R 4.0.2)                         
 htmltools              0.5.1.1    2021-01-22 [1] CRAN (R 4.0.2)                         
 htmlwidgets            1.5.3      2020-12-10 [1] CRAN (R 4.0.2)                         
 httr                   1.4.2      2020-07-20 [1] CRAN (R 4.0.2)                         
 ipred                  0.9-10     2021-03-04 [1] CRAN (R 4.0.2)                         
 IRanges                2.24.1     2020-12-12 [1] Bioconductor                           
 iterators              1.0.13     2020-10-15 [1] CRAN (R 4.0.2)                         
 jsonlite               1.7.2      2020-12-09 [1] CRAN (R 4.0.2)                         
 lattice                0.20-41    2020-04-02 [1] CRAN (R 4.0.3)                         
 lava                   1.6.8.1    2020-11-04 [1] CRAN (R 4.0.2)                         
 lazyeval               0.2.2      2019-03-15 [1] CRAN (R 4.0.0)                         
 lifecycle              1.0.0      2021-02-15 [1] CRAN (R 4.0.2)                         
 limma                  3.46.0     2020-10-27 [1] Bioconductor                           
 locfit                 1.5-9.4    2020-03-25 [1] CRAN (R 4.0.0)                         
 lubridate              1.7.10     2021-02-26 [1] CRAN (R 4.0.2)                         
 magrittr               2.0.1      2020-11-17 [1] CRAN (R 4.0.2)                         
 MASS                   7.3-53.1   2021-02-12 [1] CRAN (R 4.0.2)                         
 Matrix                 1.3-2      2021-01-06 [1] CRAN (R 4.0.2)                         
 MatrixGenerics         1.2.1      2021-01-30 [1] Bioconductor                           
 matrixStats            0.58.0     2021-01-29 [1] CRAN (R 4.0.2)                         
 memoise                2.0.0      2021-01-26 [1] CRAN (R 4.0.2)                         
 mgcv                   1.8-34     2021-02-16 [1] CRAN (R 4.0.2)                         
 ModelMetrics           1.2.2.2    2020-03-17 [1] CRAN (R 4.0.0)                         
 MultiAssayExperiment   1.16.0     2020-10-27 [1] Bioconductor                           
 munsell                0.5.0      2018-06-12 [1] CRAN (R 4.0.0)                         
 nlme                   3.1-152    2021-02-04 [1] CRAN (R 4.0.2)                         
 nnet                   7.3-15     2021-01-24 [1] CRAN (R 4.0.2)                         
 openssl                1.4.3      2020-09-18 [1] CRAN (R 4.0.2)                         
 permute                0.9-5      2019-03-12 [1] CRAN (R 4.0.0)                         
 pillar                 1.5.1      2021-03-05 [1] CRAN (R 4.0.2)                         
 pkgbuild               1.2.0      2020-12-15 [1] CRAN (R 4.0.2)                         
 pkgconfig              2.0.3      2019-09-22 [1] CRAN (R 4.0.0)                         
 pkgload                1.2.0      2021-02-23 [1] CRAN (R 4.0.2)                         
 plotly                 4.9.3      2021-01-10 [1] CRAN (R 4.0.2)                         
 plotROC                2.2.1      2018-06-23 [1] CRAN (R 4.0.0)                         
 plyr                   1.8.6      2020-03-03 [1] CRAN (R 4.0.0)                         
 prettyunits            1.1.1      2020-01-24 [1] CRAN (R 4.0.0)                         
 pROC                   1.17.0.1   2021-01-13 [1] CRAN (R 4.0.2)                         
 processx               3.4.5      2020-11-30 [1] CRAN (R 4.0.2)                         
 prodlim                2019.11.13 2019-11-17 [1] CRAN (R 4.0.0)                         
 ps                     1.6.0      2021-02-28 [1] CRAN (R 4.0.2)                         
 purrr                  0.3.4      2020-04-17 [1] CRAN (R 4.0.0)                         
 quantmod               0.4.18     2020-12-09 [1] CRAN (R 4.0.2)                         
 R6                     2.5.0      2020-10-28 [1] CRAN (R 4.0.2)                         
 RColorBrewer           1.1-2      2014-12-07 [1] CRAN (R 4.0.0)                         
 Rcpp                   1.0.6      2021-01-15 [1] CRAN (R 4.0.2)                         
 RCurl                  1.98-1.2   2020-04-18 [1] CRAN (R 4.0.0)                         
 recipes                0.1.15     2020-11-11 [1] CRAN (R 4.0.2)                         
 remotes                2.2.0      2020-07-21 [1] CRAN (R 4.0.2)                         
 rentrez                1.2.3      2020-11-10 [1] CRAN (R 4.0.2)                         
 reshape2               1.4.4      2020-04-09 [1] CRAN (R 4.0.0)                         
 reticulate             1.18       2020-10-25 [1] CRAN (R 4.0.2)                         
 rex                    1.2.0      2020-04-21 [1] CRAN (R 4.0.0)                         
 rhdf5                  2.34.0     2020-10-27 [1] Bioconductor                           
 rhdf5filters           1.2.0      2020-10-27 [1] Bioconductor                           
 Rhdf5lib               1.12.1     2021-01-26 [1] Bioconductor                           
 rlang                  0.4.10     2020-12-30 [1] CRAN (R 4.0.2)                         
 ROCR                   1.0-11     2020-05-02 [1] CRAN (R 4.0.0)                         
 rpart                  4.1-15     2019-04-12 [1] CRAN (R 4.0.3)                         
 rprojroot              2.0.2      2020-11-15 [1] CRAN (R 4.0.2)                         
 RSpectra               0.16-0     2019-12-01 [1] CRAN (R 4.0.0)                         
 RSQLite                2.2.3      2021-01-24 [1] CRAN (R 4.0.2)                         
 S4Vectors              0.28.1     2020-12-09 [1] Bioconductor                           
 scales                 1.1.1      2020-05-11 [1] CRAN (R 4.0.0)                         
 sessioninfo            1.1.1      2018-11-05 [1] CRAN (R 4.0.0)                         
 shape                  1.4.5      2020-09-13 [1] CRAN (R 4.0.2)                         
 shinyjs                2.0.0      2020-09-09 [1] CRAN (R 4.0.2)                         
 stringi                1.5.3      2020-09-09 [1] CRAN (R 4.0.2)                         
 stringr                1.4.0      2019-02-10 [1] CRAN (R 4.0.0)                         
 SummarizedExperiment   1.20.0     2020-10-27 [1] Bioconductor                           
 survival               3.2-7      2020-09-28 [1] CRAN (R 4.0.3)                         
 testthat               3.0.2      2021-02-14 [1] CRAN (R 4.0.2)                         
 tibble                 3.1.0      2021-02-25 [1] CRAN (R 4.0.2)                         
 tidyr                  1.1.3      2021-03-03 [1] CRAN (R 4.0.2)                         
 tidyselect             1.1.0      2020-05-11 [1] CRAN (R 4.0.0)                         
 timeDate               3043.102   2018-02-21 [1] CRAN (R 4.0.0)                         
 tsne                   0.1-3      2016-07-15 [1] CRAN (R 4.0.0)                         
 TTR                    0.24.2     2020-09-01 [1] CRAN (R 4.0.2)                         
 umap                   0.2.7.0    2020-11-04 [1] CRAN (R 4.0.2)                         
 usethis                2.0.1      2021-02-10 [1] CRAN (R 4.0.2)                         
 utf8                   1.1.4      2018-05-24 [1] CRAN (R 4.0.0)                         
 vctrs                  0.3.6      2020-12-17 [1] CRAN (R 4.0.2)                         
 vegan                  2.5-7      2020-11-28 [1] CRAN (R 4.0.2)                         
 viridisLite            0.3.0      2018-02-01 [1] CRAN (R 4.0.0)                         
 withr                  2.4.1      2021-01-26 [1] CRAN (R 4.0.2)                         
 XML                    3.99-0.5   2020-07-23 [1] CRAN (R 4.0.2)                         
 xtable                 1.8-4      2019-04-21 [1] CRAN (R 4.0.0)                         
 xts                    0.12.1     2020-09-09 [1] CRAN (R 4.0.2)                         
 XVector                0.30.0     2020-10-28 [1] Bioconductor                           
 zlibbioc               1.36.0     2020-10-28 [1] Bioconductor                           
 zoo                    1.8-9      2021-03-09 [1] CRAN (R 4.0.3)                         

[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library
jarrodscott commented 3 years ago

oh boy. As I hit post I realized I am running BiocManager 1.30.10! Ahhh. Maybe this is the issue. I will check.

Nope, that installs with Bioconductor version 3.12

More troubleshooting: I tried uploading the example data from here. This time I get TestFeature and Sex as the Select Target Condition: under the Biomarker tab. So there must be an issue with my data but I cannot figure out what it is.

Looks like the issue is also occurring inDiversity > Beta Diversity > Boxplot

jarrodscott commented 3 years ago

I believe the reason this was not working for me is that none of my metadata categories had <=2 states. I suggest this get documented somewhere, perhaps on the appropriate pages in the app :) especially since other biomarker discovery tools (e.g. lefse) allow for >2 states.

This issue can be closed unless it is possible to allow more than 2 states. Thanks!