Subset and plotting issue with vis_gene()

[Dimitri-Sid]

plots using the vis_gene() function are not generated:

spatialLIBD::vis_gene( spe = spe, sampleid = "panel1", geneid = "Xkr4; ENSMUSG00000051951" )

geneid references gene_search variables

sessionInfo():

R version 4.1.0 (2021-05-18) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages: [1] Matrix_1.3-3 GEOquery_2.60.0 rsconnect_0.8.18
[4] spatialLIBD_1.4.0 pryr_0.1.4 rtracklayer_1.52.0
[7] SpatialExperiment_1.2.1 SingleCellExperiment_1.14.1 SummarizedExperiment_1.22.0 [10] Biobase_2.52.0 GenomicRanges_1.44.0 GenomeInfoDb_1.28.0
[13] IRanges_2.26.0 MatrixGenerics_1.4.0 matrixStats_0.59.0
[16] BiocFileCache_2.0.0 dbplyr_2.1.1 S4Vectors_0.30.0
[19] BiocGenerics_0.38.0

loaded via a namespace (and not attached): [1] spam_2.6-0 AnnotationHub_3.0.1 lazyeval_0.2.2
[4] Polychrome_1.2.6 BiocParallel_1.26.0 scater_1.20.1
[7] usethis_2.0.1 ggplot2_3.3.4 benchmarkme_1.0.7
[10] digest_0.6.27 foreach_1.5.1 htmltools_0.5.1.1
[13] viridis_0.6.1 magick_2.7.2 fansi_0.5.0
[16] magrittr_2.0.1 memoise_2.0.0 ScaledMatrix_1.0.0
[19] config_0.3.1 doParallel_1.0.16 remotes_2.4.0
[22] limma_3.48.0 readr_1.4.0 Biostrings_2.60.1
[25] R.utils_2.10.1 colorspace_2.0-1 blob_1.2.1
[28] rappdirs_0.3.3 xfun_0.24 dplyr_1.0.7
[31] crayon_1.4.1 RCurl_1.98-1.3 jsonlite_1.7.2
[34] roxygen2_7.1.1 iterators_1.0.13 glue_1.4.2
[37] gtable_0.3.0 zlibbioc_1.38.0 XVector_0.32.0
[40] DelayedArray_0.18.0 BiocSingular_1.8.1 DropletUtils_1.12.1
[43] Rhdf5lib_1.14.1 maps_3.3.0 HDF5Array_1.20.0
[46] scales_1.1.1 DBI_1.1.1 edgeR_3.34.0
[49] Rcpp_1.0.6 viridisLite_0.4.0 xtable_1.8-4
[52] dqrng_0.3.0 rsvd_1.0.5 bit_4.0.4
[55] dotCall64_1.0-1 DT_0.18 htmlwidgets_1.5.3
[58] httr_1.4.2 RColorBrewer_1.1-2 ellipsis_0.3.2
[61] farver_2.1.0 dockerfiler_0.1.3 pkgconfig_2.0.3
[64] XML_3.99-0.6 R.methodsS3_1.8.1 scuttle_1.2.0
[67] sass_0.4.0 locfit_1.5-9.4 utf8_1.2.1
[70] labeling_0.4.2 tidyselect_1.1.1 rlang_0.4.11
[73] later_1.2.0 AnnotationDbi_1.54.1 munsell_0.5.0
[76] BiocVersion_3.13.1 tools_4.1.0 cachem_1.0.5
[79] cli_2.5.0 generics_0.1.0 RSQLite_2.2.7
[82] ExperimentHub_2.0.0 stringr_1.4.0 fastmap_1.1.0
[85] yaml_2.2.1 knitr_1.33 fs_1.5.0
[88] bit64_4.0.5 purrr_0.3.4 KEGGREST_1.32.0
[91] sparseMatrixStats_1.4.0 mime_0.10 R.oo_1.24.0
[94] xml2_1.3.2 compiler_4.1.0 rstudioapi_0.13
[97] beeswarm_0.4.0 plotly_4.9.4.1 filelock_1.0.2
[100] curl_4.3.1 png_0.1-7 interactiveDisplayBase_1.30.0 [103] testthat_3.0.3 tibble_3.1.2 bslib_0.2.5.1
[106] stringi_1.6.1 desc_1.3.0 fields_12.3
[109] lattice_0.20-44 vctrs_0.3.8 pillar_1.6.1
[112] lifecycle_1.0.0 rhdf5filters_1.4.0 BiocManager_1.30.16
[115] jquerylib_0.1.4 BiocNeighbors_1.10.0 irlba_2.3.3
[118] data.table_1.14.0 cowplot_1.1.1 bitops_1.0-7
[121] httpuv_1.6.1 R6_2.5.0 BiocIO_1.2.0
[124] promises_1.2.0.1 gridExtra_2.3 vipor_0.4.5
[127] sessioninfo_1.1.1 codetools_0.2-18 pkgload_1.2.1
[130] benchmarkmeData_1.0.4 assertthat_0.2.1 golem_0.3.1
[133] rhdf5_2.36.0 rprojroot_2.0.2 rjson_0.2.20
[136] shinyWidgets_0.6.0 withr_2.4.2 GenomicAlignments_1.28.0
[139] Rsamtools_2.8.0 GenomeInfoDbData_1.2.6 hms_1.1.0
[142] grid_4.1.0 beachmat_2.8.0 tidyr_1.1.3
[145] attempt_0.3.1 DelayedMatrixStats_1.14.0 scatterplot3d_0.3-41
[148] shiny_1.6.0 ggbeeswarm_0.6.0 restfulr_0.0.13