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Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕
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Error with plot_dimred when coloring by a feature #112

Open TJonCooper opened 3 years ago

TJonCooper commented 3 years ago

I am receiving the following error:

plot_dimred(model, feature_oi = "Camp", expression_source = object_expression, size_cells = 1, hex_cells = 24, nbins=5, plot_trajectory = FALSE)
Coloring by expression
Error in intI(i, n = d[1], dn[[1]], give.dn = FALSE) : 
  invalid character indexing

By removing different options, it's an error with "Camp" itself - the specification of the gene.

I've updated to the latest @devel branches of all dyno packages via:

devtools::install_github("dynverse/dyno@devel")

But the error persists. This code worked perfectly well until recently - on the same data currently loaded into the R environment.

> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

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

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

other attached packages:
 [1] ggsci_2.9                   DAseq_1.0.0                 msigdbr_7.4.1               SeuratDisk_0.0.0.9019       SeuratWrappers_0.3.0        wesanderson_0.3.6           reshape2_1.4.4              SingleCellExperiment_1.14.1 dyno_0.2.0                 
[10] dynwrap_1.2.2               dynplot_1.1.1               dynmethods_1.0.5.9000       dynguidelines_1.0.1         dynfeature_1.0.0            babelwhale_1.0.3            phateR_1.0.7                Rmagic_2.0.3                Matrix_1.3-4               
[19] ggplot2_3.3.5               celldex_1.2.0               SingleR_1.6.1               SummarizedExperiment_1.22.0 GenomicRanges_1.44.0        GenomeInfoDb_1.28.1         IRanges_2.26.0              S4Vectors_0.30.0            MatrixGenerics_1.4.0       
[28] matrixStats_0.59.0          stringr_1.4.0               SeuratObject_4.0.2          Seurat_4.0.3                Biobase_2.52.0              BiocGenerics_0.38.0        

loaded via a namespace (and not attached):
  [1] rsvd_1.0.5                    ica_1.0-2                     zinbwave_1.14.1               class_7.3-19                  ps_1.6.0                      foreach_1.5.1                 lmtest_0.9-38                 rprojroot_2.0.2              
  [9] glmnet_4.1-2                  crayon_1.4.1                  spatstat.core_2.2-0           MASS_7.3-54                   rhdf5filters_1.4.0            nlme_3.1-152                  rlang_0.4.11                  GA_3.2.1                     
 [17] XVector_0.32.0                caret_6.0-88                  ROCR_1.0-11                   irlba_2.3.3                   callr_3.7.0                   limma_3.48.0                  phylobase_0.8.10              filelock_1.0.2               
 [25] BiocParallel_1.26.0           dyndimred_1.0.4               bit64_4.0.5                   glue_1.4.2                    rngtools_1.5                  sctransform_0.3.2             processx_3.5.2                spatstat.sparse_2.0-0        
 [33] AnnotationDbi_1.54.0          dynutils_1.0.6                spatstat.geom_2.2-0           tidyselect_1.1.1              lmds_0.1.0                    usethis_2.0.1                 fitdistrplus_1.1-5            XML_3.99-0.6                 
 [41] tidyr_1.1.3                   zoo_1.8-9                     xtable_1.8-4                  magrittr_2.0.1                cli_3.0.0                     zlibbioc_1.38.0               rstudioapi_0.13               miniUI_0.1.1.1               
 [49] rpart_4.1-15                  locfdr_1.1-8                  shiny_1.6.0                   BiocSingular_1.8.0            pkgbuild_1.2.0                cluster_2.1.2                 tidygraph_1.2.0               KEGGREST_1.32.0              
 [57] tibble_3.1.2                  interactiveDisplayBase_1.30.0 ggrepel_0.9.1                 ape_5.5                       listenv_0.8.0                 Biostrings_2.60.0             png_0.1-7                     future_1.21.0                
 [65] ipred_0.9-11                  withr_2.4.2                   bitops_1.0-7                  ggforce_0.3.3                 ranger_0.12.1                 plyr_1.8.6                    e1071_1.7-7                   pROC_1.17.0.1                
 [73] pillar_1.6.1                  RcppParallel_5.1.4            cachem_1.0.5                  fs_1.5.0                      hdf5r_1.3.3                   kernlab_0.9-29                DelayedMatrixStats_1.14.0     vctrs_0.3.8                  
 [81] ellipsis_0.3.2                generics_0.1.0                lava_1.6.9                    devtools_2.4.2                NMF_0.23.0                    tools_4.1.0                   rncl_0.8.4                    munsell_0.5.0                
 [89] tweenr_1.0.2                  proxy_0.4-26                  DelayedArray_0.18.0           fastmap_1.1.0                 compiler_4.1.0                pkgload_1.2.1                 abind_1.4-5                   httpuv_1.6.1                 
 [97] ExperimentHub_2.0.0           sessioninfo_1.1.1             pkgmaker_0.32.2               plotly_4.9.4.1                GenomeInfoDbData_1.2.6        prodlim_2019.11.13            gridExtra_2.3                 edgeR_3.34.0                 
[105] lattice_0.20-44               deldir_0.2-10                 utf8_1.2.1                    later_1.2.0                   dplyr_1.0.7                   BiocFileCache_2.0.0           recipes_0.1.16                jsonlite_1.7.2               
[113] scales_1.1.1                  ScaledMatrix_1.0.0            pbapply_1.4-3                 sparseMatrixStats_1.4.0       genefilter_1.74.0             lazyeval_0.2.2                promises_1.2.0.1              doParallel_1.0.16            
[121] goftest_1.2-2                 spatstat.utils_2.2-0          reticulate_1.20               cowplot_1.1.1                 Rtsne_0.15                    softImpute_1.4-1              uwot_0.1.10                   igraph_1.2.6                 
[129] HDF5Array_1.20.0              proxyC_0.2.0                  survival_3.2-11               yaml_2.2.1                    carrier_0.1.0                 htmltools_0.5.1.1             memoise_2.0.0                 locfit_1.5-9.4               
[137] graphlayouts_0.7.1            viridisLite_0.4.0             digest_0.6.27                 assertthat_0.2.1              mime_0.11                     rappdirs_0.3.3                registry_0.5-1                dynparam_1.0.2               
[145] RSQLite_2.2.7                 future.apply_1.7.0            remotes_2.4.0                 data.table_1.14.0             blob_1.2.1                    RNeXML_2.4.5                  labeling_0.4.2                splines_4.1.0                
[153] Rhdf5lib_1.14.0               AnnotationHub_3.0.0           RCurl_1.98-1.3                hms_1.1.0                     rhdf5_2.36.0                  colorspace_2.0-2              BiocManager_1.30.16           shape_1.4.6                  
[161] nnet_7.3-16                   Rcpp_1.0.6                    RANN_2.6.1                    fansi_0.5.0                   parallelly_1.26.1             ModelMetrics_1.2.2.2          R6_2.5.0                      grid_4.1.0                   
[169] ggridges_0.5.3                lifecycle_1.0.0               curl_4.3.2                    leiden_0.3.8                  testthat_3.0.4                howmany_0.3-1                 desc_1.3.0                    RcppAnnoy_0.0.18             
[177] RColorBrewer_1.1-2            iterators_1.0.13              gower_0.2.2                   htmlwidgets_1.5.3             beachmat_2.8.0                polyclip_1.10-0               purrr_0.3.4                   mgcv_1.8-36                  
[185] globals_0.14.0                patchwork_1.1.1               clusterExperiment_2.12.0      codetools_0.2-18              lubridate_1.7.10              prettyunits_1.1.1             dbplyr_2.1.1                  gridBase_0.4-7               
[193] gtable_0.3.0                  DBI_1.1.1                     tensor_1.5                    httr_1.4.2                    KernSmooth_2.23-20            stringi_1.6.2                 progress_1.2.2                farver_2.1.0                 
[201] uuid_0.1-4                    annotate_1.70.0               viridis_0.6.1                 timeDate_3043.102             xml2_1.3.2                    BiocNeighbors_1.10.0          ade4_1.7-17                   readr_1.4.0                  
[209] scattermore_0.7               BiocVersion_3.13.1            bit_4.0.4                     spatstat.data_2.1-0           ggraph_2.0.5                  babelgene_21.4                pkgconfig_2.0.3
TJonCooper commented 3 years ago

All other colouring options e.g.:

plot_dimred(model, color_cells = "pseudotime")

Work as expected. And the gene is in the expression object:

which(colnames(object_expression) %in% "Camp")
[1] 289
TJonCooper commented 2 years ago

Any ideas? I can't seem to fix this issue.

rcannood commented 2 years ago

Hi @TJonCooper !

Could you provide a reproducible example for me to work with?

Kind regards, Robrecht