scatter plots -> Error in as.data.frame.default

[smovahedi]

Hi

When I run sleuth_live(so), the tab for "scatter plots" gives this error (only for the first plot):

Error in as.data.frame.default: cannot coerce class "c("quosure", "formula")" to a data.frame

How can I solve this problem?

Thanks Sara

[warrenmcg]

Hi @smovahedi,

I am not reproducing this error on my end. A few questions:

1. To be clear, the plot getting the error is the top one? And it never goes away no matter what inputs you give?
2. Do you still have an error if you do the plot function directly? What happens if you do plot_scatter(so) or plot_vars(so)?
3. What's your sessionInfo() output?
4. Can you print out the result of this command: dplyr::as_tibble(so$sample_to_covariates)?

[smovahedi]

Hi @warrenmcg

1. yes only the top one, and this is my only problem. I didn't try other data!
2. plot_scatter(so) and plot_vars(so) both generate plots without any problem.
3. here it is:

sessionInfo() R version 3.4.0 (2017-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.5 LTS

Matrix products: default BLAS: /home/BLA/programs/R/R-3.4.0/lib/R/lib/libRblas.so LAPACK: /home/BLA/programs/R/R-3.4.0/lib/R/lib/libRlapack.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=nl_NL.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=nl_NL.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=nl_NL.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=nl_NL.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] SomaticSignatures_2.10.0 VariantAnnotation_1.20.3
[3] Rsamtools_1.26.2 Biostrings_2.42.1
[5] XVector_0.14.1 SummarizedExperiment_1.4.0 [7] Biobase_2.34.0 GenomicRanges_1.26.4
[9] GenomeInfoDb_1.10.3 IRanges_2.8.2
[11] S4Vectors_0.12.2 BiocGenerics_0.20.0
[13] BiocInstaller_1.24.0 shiny_1.1.0
[15] bindrcpp_0.2.2 cowplot_0.9.3
[17] ggplot2_3.0.0 sleuth_0.30.0

loaded via a namespace (and not attached): [1] colorspace_1.3-2 biovizBase_1.22.0
[3] htmlTable_1.12 base64enc_0.1-3
[5] dichromat_2.0-0 proxy_0.4-22
[7] rstudioapi_0.7 bit64_0.9-7
[9] interactiveDisplayBase_1.12.0 AnnotationDbi_1.36.2
[11] codetools_0.2-15 splines_3.4.0
[13] ggbio_1.22.4 doParallel_1.0.11
[15] knitr_1.20 Formula_1.2-3
[17] jsonlite_1.5 Cairo_1.5-9
[19] gridBase_0.4-7 cluster_2.0.7-1
[21] pheatmap_1.0.10 graph_1.52.0
[23] compiler_3.4.0 httr_1.3.1
[25] backports_1.1.2 assertthat_0.2.0
[27] Matrix_1.2-14 lazyeval_0.2.1
[29] later_0.7.3 acepack_1.4.1
[31] htmltools_0.3.6 tools_3.4.0
[33] gtable_0.2.0 glue_1.3.0
[35] reshape2_1.4.3 dplyr_0.7.6
[37] Rcpp_0.12.17 NMF_0.21.0
[39] rtracklayer_1.34.2 iterators_1.0.10
[41] stringr_1.3.1 mime_0.5
[43] ensembldb_1.6.2 rngtools_1.3.1
[45] XML_3.98-1.12 AnnotationHub_2.6.5
[47] zlibbioc_1.20.0 scales_0.5.0
[49] BSgenome_1.42.0 pcaMethods_1.66.0
[51] promises_1.0.1 RBGL_1.50.0
[53] rhdf5_2.18.0 RColorBrewer_1.1-2
[55] yaml_2.1.19 memoise_1.1.0
[57] gridExtra_2.3 pkgmaker_0.27
[59] biomaRt_2.30.0 rpart_4.1-13
[61] reshape_0.8.7 latticeExtra_0.6-28
[63] stringi_1.2.3 RSQLite_2.1.1
[65] foreach_1.4.4 checkmate_1.8.5
[67] GenomicFeatures_1.26.4 bibtex_0.4.2
[69] BiocParallel_1.8.2 rlang_0.2.1
[71] pkgconfig_2.0.1 bitops_1.0-6
[73] lattice_0.20-35 purrr_0.2.5
[75] bindr_0.1.1 GenomicAlignments_1.10.1
[77] htmlwidgets_1.2 labeling_0.3
[79] bit_1.1-14 tidyselect_0.2.4
[81] GGally_1.4.0 plyr_1.8.4
[83] magrittr_1.5 R6_2.2.2
[85] Hmisc_4.1-1 DBI_1.0.0
[87] pillar_1.3.0 foreign_0.8-70
[89] withr_2.1.2 survival_2.42-6
[91] RCurl_1.95-4.11 nnet_7.3-12
[93] tibble_1.4.2 crayon_1.3.4
[95] OrganismDbi_1.16.0 grid_3.4.0
[97] data.table_1.11.4 blob_1.1.1
[99] digest_0.6.15 xtable_1.8-2
[101] tidyr_0.8.1 httpuv_1.4.5
[103] munsell_0.5.0 registry_0.5
[105] tcltk_3.4.0

4. here is what I get:

A tibble: 10 x 2

sample protocol
1 RNAseq01 B
2 RNAseq02 B
3 RNAseq03 B
4 RNAseq04 B
5 RNAseq05 B
6 RNAseq06 KE
7 RNAseq07 KE
8 RNAseq08 KE
9 RNAseq09 KE
10 RNAseq10 KE

[warrenmcg]

Hi @smovahedi,

I am not reproducing this error using the same set of package versions, but with R 3.3, so either it has something to do with R 3.4 or an unusual clash of variables. Two additional questions:

1. When you get the error in sleuth_live, what does the full traceback on the console say?
2. Could you print out the result of ls()?

[smovahedi]

Hi @warrenmcg

1. this is what I get:

sleuth_live(so)

Listening on http://127.0.0.*** Warning: Error in as.data.frame.default: cannot coerce class "c("quosure", "formula")" to a data.frame [No stack trace available]

2. ls() [1] "base_dir" "diff_exp" "kal_dirs" "maxb"
   [5] "minb" "results_ordered" "results_table" "s2c"
   [9] "s2c_table" "sample_id" "so" "t2g"

[warrenmcg]

Hi @smovahedi,

Apologies for the long delay in responding. I have reproduced the error, and I have identified the problem. We will work on a patch for the next release. As soon as the patch is ready, I'll let you know how you can test the devel version with the patch included.

[warrenmcg]

Ok, I have working patch ready for you to use @smovahedi.

To use this version of sleuth, do the following:

library(devtools)
install_github('warrenmcg/sleuth', ref = 'd733061') # edited with correct commit

That should install the patched version of sleuth that fixes your problem. This has all known shiny errors fixed, so give it a whirl and let us know if it works for you!

[ak-watson]

Sorry for reviving this, but has this fix been added to the main sleuth release yet?

I am just encountering the same error trying to generate diagnostic scatter plots in sleuth_live (along with a bunch of others elsewhere that I am busy troubleshooting).

Currently working in R 4.03

[msierk]

I am also seeing this error, R 4.04, even after installing the commit referenced above...

Console traceback: Warning: Error in as.data.frame.default: cannot coerce class ‘c("quosure", "formula")’ to a data.frame 174: stop 173: as.data.frame.default 171: data.frame 170: renderPlot 168: func 128: drawPlot 114: reactive:plotObj 98: drawReactive 85: renderFunc 84: output$scatter 4: runApp 3: print.shiny.appobj 1: source