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mani2012 / BatchQC

Provides Quality Control of sequencing samples by deducing if there is batch effect and adjusts for it.
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Error running analyses in the shiny app #18

Open marykthompson opened 3 years ago

marykthompson commented 3 years ago

Hi,

This looks like a really nice package, but I'm having some trouble even running the examples in the interactive mode: https://bioconductor.org/packages/release/bioc/vignettes/BatchQC/inst/doc/BatchQCIntro.html. Running the first example (Simulate data and Apply BatchQC), the app opens, but then if I try to apply ComBat or SVA, it fails to show the output, with the error shown in the shiny window: "Error: argument "p" is missing, with no default".

The RStudio console reads as follows:

Quitting from lines 105-115 (batchqc_report.Rmd)

Warning: Error in graphics::layout: argument "p" is missing, with no default 163: graphics::layout 162: layout.matrix 142: eventReactiveHandler [/usr/local/lib/R/4.0/site-library/BatchQC/shiny/BatchQC/server.R#1013] 98: combatOutText 97: renderText [/usr/local/lib/R/4.0/site-library/BatchQC/shiny/BatchQC/server.R#1021] 96: func 83: origRenderFunc 82: output$combatOutText 2: shiny::runApp 1: batchQC

I realize this may be something about my installation/setup but I have no idea how to fix it and I'd really like to use the app. Any advice is appreciated. Thanks!

sessionInfo() R version 4.0.2 (2020-06-22) Platform: x86_64-apple-darwin18.7.0 (64-bit) Running under: macOS Mojave 10.14.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /usr/local/Cellar/openblas/0.3.10_1/lib/libopenblasp-r0.3.10.dylib

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

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

other attached packages: [1] sva_3.36.0 BiocParallel_1.22.0 genefilter_1.70.0 mgcv_1.8-33
[5] nlme_3.1-149 Matrix_1.2-18 limma_3.44.3 reshape2_1.4.4
[9] heatmaply_1.1.1 viridis_0.5.1 viridisLite_0.3.0 plotly_4.9.2.1
[13] ggplot2_3.3.2 ggvis_0.4.6 pander_0.6.3 shiny_1.5.0
[17] BatchQC_1.16.2

loaded via a namespace (and not attached): [1] BiocFileCache_1.12.1 plyr_1.8.6
[3] lazyeval_0.2.2 splines_4.0.2
[5] GenomeInfoDb_1.24.2 digest_0.6.25
[7] foreach_1.5.0 htmltools_0.5.0
[9] gdata_2.18.0 magrittr_1.5
[11] memoise_1.1.0 Biostrings_2.56.0
[13] annotate_1.66.0 matrixStats_0.56.0
[15] MCMCpack_1.4-9 askpass_1.1
[17] prettyunits_1.1.1 colorspace_1.4-1
[19] blob_1.2.1 rappdirs_0.3.1
[21] xfun_0.17 dplyr_1.0.2
[23] crayon_1.3.4 RCurl_1.98-1.2
[25] jsonlite_1.7.1 survival_3.2-3
[27] iterators_1.0.12 glue_1.4.2
[29] registry_0.5-1 gtable_0.3.0
[31] zlibbioc_1.34.0 XVector_0.28.0
[33] webshot_0.5.2 MatrixModels_0.4-1
[35] DelayedArray_0.14.1 BiocGenerics_0.34.0
[37] SparseM_1.78 scales_1.1.1
[39] DBI_1.1.0 edgeR_3.30.3
[41] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 Rcpp_1.0.5
[43] xtable_1.8-4 progress_1.2.2
[45] bit_4.0.4 deSolve_1.28
[47] stats4_4.0.2 htmlwidgets_1.5.1
[49] httr_1.4.2 gplots_3.1.0
[51] RColorBrewer_1.1-2 ellipsis_0.3.1
[53] pkgconfig_2.0.3 XML_3.99-0.5
[55] dbplyr_1.4.4 locfit_1.5-9.4
[57] tidyselect_1.1.0 rlang_0.4.7
[59] later_1.1.0.1 AnnotationDbi_1.50.3
[61] munsell_0.5.0 tools_4.0.2
[63] generics_0.0.2 moments_0.14
[65] RSQLite_2.2.0 evaluate_0.14
[67] stringr_1.4.0 fastmap_1.0.1
[69] yaml_2.2.1 mcmc_0.9-7
[71] knitr_1.29 bit64_4.0.2
[73] caTools_1.18.0 plgem_1.60.0
[75] purrr_0.3.4 dendextend_1.14.0
[77] rootSolve_1.8.2.1 mime_0.9
[79] quantreg_5.73 biomaRt_2.44.1
[81] compiler_4.0.2 rstudioapi_0.11
[83] curl_4.3 tibble_3.0.3
[85] geneplotter_1.66.0 stringi_1.4.6
[87] GenomicFeatures_1.40.1 lattice_0.20-41
[89] vctrs_0.3.3 pillar_1.4.6
[91] lifecycle_0.2.0 data.table_1.13.0
[93] bitops_1.0-6 conquer_1.0.2
[95] corpcor_1.6.9 seriation_1.2-9
[97] httpuv_1.5.4 rtracklayer_1.48.0
[99] GenomicRanges_1.40.0 R6_2.4.1
[101] promises_1.1.1 TSP_1.1-10
[103] KernSmooth_2.23-17 gridExtra_2.3
[105] IRanges_2.22.2 codetools_0.2-16
[107] MASS_7.3-52 gtools_3.8.2
[109] assertthat_0.2.1 SummarizedExperiment_1.18.2
[111] openssl_1.4.2 DESeq2_1.28.1
[113] withr_2.2.0 GenomicAlignments_1.24.0
[115] Rsamtools_2.4.0 S4Vectors_0.26.1
[117] GenomeInfoDbData_1.2.3 hms_0.5.3
[119] grid_4.0.2 tidyr_1.1.2
[121] coda_0.19-4 rmarkdown_2.3
[123] pROC_1.16.2 Biobase_2.48.0

mani2012 commented 3 years ago

Hi,

Thanks for your message. I just fixed this and committed the changes. This should be fixed in the next build in a day or two. Please let me know if you still have any issues after updating the package.

Best, Mani

From: marykthompson notifications@github.com Sent: Thursday, October 8, 2020 9:07 AM To: mani2012/BatchQC BatchQC@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [mani2012/BatchQC] Error running analyses in the shiny app (#18)

Hi,

This looks like a really nice package, but I'm having some trouble even running the examples in the interactive mode: https://bioconductor.org/packages/release/bioc/vignettes/BatchQC/inst/doc/BatchQCIntro.html. Running the first example (Simulate data and Apply BatchQC), the app opens, but then if I try to apply ComBat or SVA, it fails to show the output, with the error shown in the shiny window: "Error: argument "p" is missing, with no default".

The RStudio console reads as follows:

Quitting from lines 105-115 (batchqc_report.Rmd)

Warning: Error in graphics::layout: argument "p" is missing, with no default 163: graphics::layout 162: layout.matrix 142: eventReactiveHandler [/usr/local/lib/R/4.0/site-library/BatchQC/shiny/BatchQC/server.R#1013] 98: combatOutText 97: renderText [/usr/local/lib/R/4.0/site-library/BatchQC/shiny/BatchQC/server.R#1021] 96: func 83: origRenderFunc 82: output$combatOutText 2: shiny::runApp 1: batchQC

I realize this may be something about my installation/setup but I have no idea how to fix it and I'd really like to use the app. Any advice is appreciated. Thanks!

sessionInfo() R version 4.0.2 (2020-06-22) Platform: x86_64-apple-darwin18.7.0 (64-bit) Running under: macOS Mojave 10.14.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /usr/local/Cellar/openblas/0.3.10_1/lib/libopenblasp-r0.3.10.dylib

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

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

other attached packages: [1] sva_3.36.0 BiocParallel_1.22.0 genefilter_1.70.0 mgcv_1.8-33 [5] nlme_3.1-149 Matrix_1.2-18 limma_3.44.3 reshape2_1.4.4 [9] heatmaply_1.1.1 viridis_0.5.1 viridisLite_0.3.0 plotly_4.9.2.1 [13] ggplot2_3.3.2 ggvis_0.4.6 pander_0.6.3 shiny_1.5.0 [17] BatchQC_1.16.2

loaded via a namespace (and not attached): [1] BiocFileCache_1.12.1 plyr_1.8.6 [3] lazyeval_0.2.2 splines_4.0.2 [5] GenomeInfoDb_1.24.2 digest_0.6.25 [7] foreach_1.5.0 htmltools_0.5.0 [9] gdata_2.18.0 magrittr_1.5 [11] memoise_1.1.0 Biostrings_2.56.0 [13] annotate_1.66.0 matrixStats_0.56.0 [15] MCMCpack_1.4-9 askpass_1.1 [17] prettyunits_1.1.1 colorspace_1.4-1 [19] blob_1.2.1 rappdirs_0.3.1 [21] xfun_0.17 dplyr_1.0.2 [23] crayon_1.3.4 RCurl_1.98-1.2 [25] jsonlite_1.7.1 survival_3.2-3 [27] iterators_1.0.12 glue_1.4.2 [29] registry_0.5-1 gtable_0.3.0 [31] zlibbioc_1.34.0 XVector_0.28.0 [33] webshot_0.5.2 MatrixModels_0.4-1 [35] DelayedArray_0.14.1 BiocGenerics_0.34.0 [37] SparseM_1.78 scales_1.1.1 [39] DBI_1.1.0 edgeR_3.30.3 [41] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 Rcpp_1.0.5 [43] xtable_1.8-4 progress_1.2.2 [45] bit_4.0.4 deSolve_1.28 [47] stats4_4.0.2 htmlwidgets_1.5.1 [49] httr_1.4.2 gplots_3.1.0 [51] RColorBrewer_1.1-2 ellipsis_0.3.1 [53] pkgconfig_2.0.3 XML_3.99-0.5 [55] dbplyr_1.4.4 locfit_1.5-9.4 [57] tidyselect_1.1.0 rlang_0.4.7 [59] later_1.1.0.1 AnnotationDbi_1.50.3 [61] munsell_0.5.0 tools_4.0.2 [63] generics_0.0.2 moments_0.14 [65] RSQLite_2.2.0 evaluate_0.14 [67] stringr_1.4.0 fastmap_1.0.1 [69] yaml_2.2.1 mcmc_0.9-7 [71] knitr_1.29 bit64_4.0.2 [73] caTools_1.18.0 plgem_1.60.0 [75] purrr_0.3.4 dendextend_1.14.0 [77] rootSolve_1.8.2.1 mime_0.9 [79] quantreg_5.73 biomaRt_2.44.1 [81] compiler_4.0.2 rstudioapi_0.11 [83] curl_4.3 tibble_3.0.3 [85] geneplotter_1.66.0 stringi_1.4.6 [87] GenomicFeatures_1.40.1 lattice_0.20-41 [89] vctrs_0.3.3 pillar_1.4.6 [91] lifecycle_0.2.0 data.table_1.13.0 [93] bitops_1.0-6 conquer_1.0.2 [95] corpcor_1.6.9 seriation_1.2-9 [97] httpuv_1.5.4 rtracklayer_1.48.0 [99] GenomicRanges_1.40.0 R6_2.4.1 [101] promises_1.1.1 TSP_1.1-10 [103] KernSmooth_2.23-17 gridExtra_2.3 [105] IRanges_2.22.2 codetools_0.2-16 [107] MASS_7.3-52 gtools_3.8.2 [109] assertthat_0.2.1 SummarizedExperiment_1.18.2 [111] openssl_1.4.2 DESeq2_1.28.1 [113] withr_2.2.0 GenomicAlignments_1.24.0 [115] Rsamtools_2.4.0 S4Vectors_0.26.1 [117] GenomeInfoDbData_1.2.3 hms_0.5.3 [119] grid_4.0.2 tidyr_1.1.2 [121] coda_0.19-4 rmarkdown_2.3 [123] pROC_1.16.2 Biobase_2.48.0

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joshua-theisen commented 3 years ago

I think I'm having a related problem. In the Shiny app, in the Summary > P-value Analysis tab, there is no graph of p-values but the message Error: argument "p" is missing, with no default. The error occurs with both the simulated data and the signature data. In the RStudio console has this at the end:

Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-33. For overview type 'help("mgcv-package")'.
Loading required package: genefilter
Loading required package: BiocParallel
Warning: Error in graphics::layout: argument "p" is missing, with no default
  171: graphics::layout
  170: layout.matrix
  168: renderPlot [C:\Users\JT\Documents\R\win-library\4.0\BatchQC\shiny\BatchQC/server.R#185]
  166: func
  126: drawPlot
  112: <reactive:plotObj>
   96: drawReactive
   83: renderFunc
   82: output$BatchPvaluePlot
    2: shiny::runApp
    1: batchQC
Warning: Error in graphics::layout: argument "p" is missing, with no default
  171: graphics::layout
  170: layout.matrix
  168: renderPlot [C:\Users\JT\Documents\R\win-library\4.0\BatchQC\shiny\BatchQC/server.R#212]
  166: func
  126: drawPlot
  112: <reactive:plotObj>
   96: drawReactive
   83: renderFunc
   82: output$ConditionPvaluePlot
    2: shiny::runApp
    1: batchQC

Is there a fix for this? Is it related to this question about incompatibility between the plotly and formattable packages? https://stackoverflow.com/questions/56840172/r-shiny-error-in-plotly-build-argument-p-missing-with-no-default-value/57081424

Thanks for your help.