PoisonAlien
plotmafSummary version dependent error
Hi, I'm running the same app in two different machines, my laptop and a workstation. In one, the code works just fine, in the second one, it fails with the following error:
Warning: Error in graphics::layout: argument "p" is missing, with no default
97: graphics::layout
96: layout.matrix
94: dashboard
93: plotmafSummary
89: <reactive:procesar_info> [tab_filtrado.R#66]
73: procesar_info
72: observeEventHandler [tab_filtrado.R#47]
1: runApp
The offending lines are:
info.maf <- readMaf(nombre_usar)
maf.plotsum <- plotmafSummary(info.maf, addStat = 'median', dashboard = TRUE)
The MAF file (info.maf) is correctly read:
>print(info.maf)
An object of class MAF
ID summary Mean Median
1: NCBI_Build GRCh37 NA NA
2: Center . NA NA
3: Samples 1 NA NA
4: nGenes 36 NA NA
5: Frame_Shift_Del 1 1 1
6: Missense_Mutation 51 51 51
7: Splice_Site 2 2 2
8: total 54 54 54
It seems that there is some change in the signature of the underlying function graphics::layout
R sessionInfo() for the workstation (running ok):
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /opt/R-3.4.3/lib/libRblas.so
LAPACK: /opt/R-3.4.3/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=es_AR.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=es_AR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=es_AR.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] maftools_1.4.28 Biobase_2.38.0 BiocGenerics_0.24.0
loaded via a namespace (and not attached):
[1] bitops_1.0-6 matrixStats_0.53.1
[3] bit64_0.9-7 doParallel_1.0.11
[5] RColorBrewer_1.1-2 progress_1.1.2
[7] httr_1.3.1 GenomeInfoDb_1.14.0
[9] tools_3.4.3 R6_2.3.0
[11] DBI_0.8 lazyeval_0.2.1
[13] colorspace_1.3-2 GetoptLong_0.1.6
[15] gridExtra_2.3 prettyunits_1.0.2
[17] RMySQL_0.10.14 bit_1.1-12
[19] compiler_3.4.3 DelayedArray_0.4.1
[21] pkgmaker_0.22 slam_0.1-42
[23] rtracklayer_1.38.3 scales_1.0.0
[25] NMF_0.21.0 stringr_1.3.1
[27] digest_0.6.18 Rsamtools_1.30.0
[29] XVector_0.18.0 pkgconfig_2.0.1
[31] changepoint_2.2.2 BSgenome_1.46.0
[33] rlang_0.3.0.1 GlobalOptions_0.0.13
[35] RSQLite_2.0 shape_1.4.4
[37] bindr_0.1.1 zoo_1.8-1
[39] mclust_5.4 BiocParallel_1.12.0
[41] dplyr_0.7.4 VariantAnnotation_1.24.5
[43] RCurl_1.95-4.10 magrittr_1.5
[45] GenomeInfoDbData_1.0.0 wordcloud_2.5
[47] Matrix_1.2-12 Rcpp_0.12.19
[49] munsell_0.5.0 S4Vectors_0.16.0
[51] stringi_1.1.7 SummarizedExperiment_1.8.1
[53] zlibbioc_1.24.0 plyr_1.8.4
[55] grid_3.4.3 blob_1.1.1
[57] ggrepel_0.7.0 lattice_0.20-35
[59] Biostrings_2.46.0 cowplot_0.9.2
[61] splines_3.4.3 GenomicFeatures_1.30.3
[63] circlize_0.4.3 ComplexHeatmap_1.17.1
[65] pillar_1.2.1 GenomicRanges_1.30.3
[67] rjson_0.2.15 rngtools_1.2.4
[69] reshape2_1.4.3 codetools_0.2-15
[71] biomaRt_2.34.2 stats4_3.4.3
[73] XML_3.98-1.10 glue_1.2.0
[75] data.table_1.10.4-3 foreach_1.4.4
[77] gtable_0.2.0 assertthat_0.2.0
[79] ggplot2_3.1.0.9000 gridBase_0.4-7
[81] xtable_1.8-2 survival_2.41-3
[83] tibble_1.4.2 iterators_1.0.9
[85] GenomicAlignments_1.14.1 AnnotationDbi_1.40.0
[87] registry_0.5 memoise_1.1.0
[89] IRanges_2.12.0 bindrcpp_0.2
[91] cluster_2.0.6
R sessionInfo() for the laptop (showing this error):
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 19
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=es_AR.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=es_AR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=es_AR.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] maftools_1.8.10 Biobase_2.42.0 BiocGenerics_0.28.0
loaded via a namespace (and not attached):
[1] splines_3.5.1 foreach_1.4.4
[3] assertthat_0.2.0 stats4_3.5.1
[5] BSgenome_1.50.0 GenomeInfoDbData_1.2.0
[7] Rsamtools_1.34.0 ggrepel_0.8.0
[9] pillar_1.3.0 lattice_0.20-38
[11] glue_1.3.0 digest_0.6.18
[13] GenomicRanges_1.34.0 RColorBrewer_1.1-2
[15] XVector_0.22.0 colorspace_1.3-2
[17] cowplot_0.9.3 Matrix_1.2-15
[19] plyr_1.8.4 XML_3.98-1.16
[21] pkgconfig_2.0.2 bibtex_0.4.2
[23] GetoptLong_0.1.7 zlibbioc_1.28.0
[25] purrr_0.2.5 xtable_1.8-3
[27] scales_1.0.0 BiocParallel_1.16.0
[29] tibble_1.4.2 pkgmaker_0.27
[31] IRanges_2.16.0 ggplot2_3.1.0
[33] withr_2.1.2 SummarizedExperiment_1.12.0
[35] lazyeval_0.2.1 survival_2.43-1
[37] magrittr_1.5 crayon_1.3.4
[39] mclust_5.4.2 doParallel_1.0.14
[41] NMF_0.21.0 tools_3.5.1
[43] registry_0.5 data.table_1.11.8
[45] GlobalOptions_0.1.0 matrixStats_0.54.0
[47] gridBase_0.4-7 ComplexHeatmap_1.20.0
[49] stringr_1.3.1 S4Vectors_0.20.0
[51] munsell_0.5.0 cluster_2.0.7-1
[53] rngtools_1.3.1 DelayedArray_0.8.0
[55] bindrcpp_0.2.2 Biostrings_2.50.0
[57] compiler_3.5.1 GenomeInfoDb_1.18.0
[59] rlang_0.3.0.1 grid_3.5.1
[61] RCurl_1.95-4.11 iterators_1.0.10
[63] rjson_0.2.20 circlize_0.4.5
[65] bitops_1.0-6 gtable_0.2.0
[67] codetools_0.2-15 reshape2_1.4.3
[69] R6_2.3.0 GenomicAlignments_1.18.0
[71] gridExtra_2.3 dplyr_0.7.8
[73] rtracklayer_1.42.0 bindr_0.1.1
[75] shape_1.4.4 stringi_1.2.4
[77] Rcpp_1.0.0 wordcloud_2.6
[79] tidyselect_0.2.5
Hi @diegollarrull ,
Please accept my apologies for late reply as I was on vacation. plotMafSummary function had ggplot code in version 1.4 but later migrated to base R after 1.6. Regardless they should work fine. Problem here is, you have only one sample. Most of maftools function won't work with single sample - could you please try with more samples and see if it helps ?
Hi @PoisonAlien , I have the same issue.
I am tempted to use v1.4. Is there any reason I should no of not to do so?
Thanks in advance.
Hi @cgpu , Sorry for the late reply. Do you still have the issue? You should definitely update the package since v1.4 is way too old.
Hey @PoisonAlien, thanks for the reply much appreciated. Still have the issue, I was very tempted to use the old old version because of ggplot 😄 but I have conflicts with other packages so I put this in icebox atm.
I swear that when I run the first few plots it worked, but when I knit I get this:
## Error in graphics::layout(p, ...): argument "p" is missing, with no default
The weird thing is some of the plots look fine (eg the bottom one here).
Have you come across this again?
If you have a working example, would you mind sharing the sessionInfo so I can check the package versions?
Thanks for the help! Christina
Ah! Okat, This issue similar to #387
Loading plotly conflicts with layout function from base. I will take care of it soon :)
Ah! Okat, This issue similar to #387 Loading
plotlyconflicts withlayoutfunction from base. I will take care of it soon :)
Ah that's awesome news - I can afford to not include plotly actually for this iteration so all good! Thank you for the help and such a prompt response. Feel free to use me as a tester for any update, would be happy to help if I can.