show_pdata errors in sc3_plot_expression(), sc3_plot_de_genes(), sc3_plot_markers(), but not sc3_plot_consensus()

KeelyDulmage commented 6 years ago

I can't get annotation info in show_pdata to work in most of the sc3_plot functions. The heatmaps plot just fine until I try to enable the show_pdata method. I get errors in both RStudio and in the SC3 gui. Different errors though. This is what it looks like in RStudio:

Here's the one that works:

Errors in Shiny:

Package/Session info:

Thanks!

wikiselev commented 6 years ago

Could you please share your dataset with me (vk6@sanger.ac.uk), so that I can reproduce?

astrid12345 commented 6 years ago

I have the exact same issue. Did you come across a solution already?

Thank you!

astrid12345 commented 6 years ago

Also, get_marker_genes(sce) gives Error in as.vector(x) : no method for coercing this S4 class to a vector

sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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

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

other attached packages: [1] SC3_1.7.7 scran_1.6.9 BiocParallel_1.12.0 mgcv_1.8-23 nlme_3.1-131 tibble_1.4.2
[7] scater_1.6.3 ggplot2_2.2.1 SingleCellExperiment_1.0.0 SummarizedExperiment_1.8.1 DelayedArray_0.4.1 matrixStats_0.53.1
[13] Biobase_2.38.0 GenomicRanges_1.30.3 GenomeInfoDb_1.14.0 IRanges_2.12.0 S4Vectors_0.16.0 BiocGenerics_0.24.0
[19] BiocInstaller_1.28.0

loaded via a namespace (and not attached): [1] ggbeeswarm_0.6.0 colorspace_1.3-2 rjson_0.2.19 class_7.3-14 dynamicTreeCut_1.63-1 XVector_0.18.0 DT_0.4
[8] bit64_0.9-7 mvtnorm_1.0-7 AnnotationDbi_1.40.0 codetools_0.2-15 tximport_1.6.0 doParallel_1.0.11 robustbase_0.93-0
[15] cluster_2.0.6 pheatmap_1.0.10 shinydashboard_0.7.0 shiny_1.1.0 rrcov_1.4-4 compiler_3.4.4 httr_1.3.1
[22] assertthat_0.2.0 Matrix_1.2-14 lazyeval_0.2.1 limma_3.34.9 later_0.7.2 htmltools_0.3.6 prettyunits_1.0.2
[29] tools_3.4.4 bindrcpp_0.2.2 igraph_1.2.1 gtable_0.2.0 glue_1.2.0 GenomeInfoDbData_1.0.0 reshape2_1.4.3
[36] dplyr_0.7.5 doRNG_1.6.6 Rcpp_0.12.17 gdata_2.18.0 iterators_1.0.9 stringr_1.3.1 mime_0.5
[43] rngtools_1.3.1 gtools_3.5.0 WriteXLS_4.0.0 statmod_1.4.30 XML_3.98-1.11 DEoptimR_1.0-8 edgeR_3.20.9
[50] zlibbioc_1.24.0 zoo_1.8-1 scales_0.5.0 promises_1.0.1 rhdf5_2.22.0 RColorBrewer_1.1-2 memoise_1.1.0
[57] gridExtra_2.3 pkgmaker_0.27 biomaRt_2.34.2 stringi_1.2.2 RSQLite_2.1.1 pcaPP_1.9-73 foreach_1.4.4
[64] e1071_1.6-8 caTools_1.17.1 bibtex_0.4.2 rlang_0.2.0 pkgconfig_2.0.1 bitops_1.0-6 lattice_0.20-35
[71] ROCR_1.0-7 purrr_0.2.4 bindr_0.1.1 htmlwidgets_1.2 labeling_0.3 cowplot_0.9.2 bit_1.1-13
[78] tidyselect_0.2.4 plyr_1.8.4 magrittr_1.5 R6_2.2.2 gplots_3.0.1 DBI_1.0.0 pillar_1.2.3
[85] withr_2.1.2 RCurl_1.95-4.10 KernSmooth_2.23-15 viridis_0.5.1 progress_1.1.2 locfit_1.5-9.1 grid_3.4.4
[92] data.table_1.11.4 blob_1.1.1 FNN_1.1 digest_0.6.15 xtable_1.8-2 httpuv_1.4.3 munsell_0.4.3
[99] beeswarm_0.2.3 registry_0.5 viridisLite_0.3.0 vipor_0.4.5

wikiselev commented 6 years ago

Could you please share your dataset with me (vk6@sanger.ac.uk), so that I can reproduce?

hemberg-lab / SC3

show_pdata errors in sc3_plot_expression(), sc3_plot_de_genes(), sc3_plot_markers(), but not sc3_plot_consensus() #65