plot.states.radar plotting error with ggplot2 >= 3.5.0

[Shiywa]

Hi, thanks for your great work on this package!
I would like to report a bug that occurs when using the plot.states.radar() function with the latest versions of ggplot2 (>= 3.5.0).

[mass-a]

Hi,
thanks for reporting.
Can you tell us what is the behavior, and what is the sessionInfo() to reproduce it?

[nandini0910]

Is this the error you got?

Although my seurat object is of mouse data, I used this tutorial because I wanted the same annotations. https://carmonalab.github.io/ProjecTILs_CaseStudies/Bassez_BC.html#content

`> plot.states.radar(ref = ref.cd4, query = CD4)
Error in ..subscript.2ary(x, l[[1L]], l[[2L]], drop = drop[1L]) :
NA subscripts in x[i,j] not supported for 'x' inheriting from sparseMatrix

sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Red Hat Enterprise Linux 8.10 (Ootpa)

Matrix products: default
BLAS: /apps/R/4.4.0/lib64/R/lib/libRblas.so
LAPACK: /apps/R/4.4.0/lib64/R/lib/libRlapack.so; LAPACK version 3.12.0

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

time zone: America/Los_Angeles
tzcode source: system (glibc)

attached base packages:
[1] splines grid stats graphics grDevices utils datasets methods base

other attached packages:
[1] ProjecTILs_3.6.0 DoubletFinder_2.0.6 clustree_0.5.1 ggraph_2.2.2 tibble_3.3.0
[6] SeuratDisk_0.0.0.9021 Seurat_5.3.1 SeuratObject_5.2.0 sp_2.2-0 VennDiagram_1.7.3
[11] futile.logger_1.4.3 ggvenn_0.1.19 reshape2_1.4.5 readr_2.1.5 ggrepel_0.9.6
[16] ggforce_0.5.0 stringr_1.6.0 pheatmap_1.0.13 gam_1.22-6 foreach_1.5.2
[21] ggbeeswarm_0.7.2 ggthemes_5.1.0 gmodels_2.19.1 multcomp_1.4-28 TH.data_1.1-4
[26] MASS_7.3-65 survival_3.8-3 mvtnorm_1.3-3 lme4_1.1-37 Matrix_1.7-4
[31] ggtext_0.1.2 scales_1.4.0 gridExtra_2.3 tidyr_1.3.1 ConsensusClusterPlus_1.68.0
[36] limma_3.60.6 readxl_1.4.5 ComplexHeatmap_2.20.0 RColorBrewer_1.1-3 openxlsx_4.2.8.1
[41] patchwork_1.3.2 ggplot2_4.0.1 dplyr_1.1.4 cowplot_1.2.0

loaded via a namespace (and not attached):
[1] matrixStats_1.5.0 spatstat.sparse_3.1-0 httr_1.4.7 doParallel_1.0.17
[5] tools_4.4.0 sctransform_0.4.2 R6_2.6.1 lazyeval_0.2.2
[9] uwot_0.2.4 GetoptLong_1.0.5 withr_3.0.2 progressr_0.18.0
[13] cli_3.6.5 Biobase_2.64.0 formatR_1.14 spatstat.explore_3.6-0
[17] fastDummies_1.7.5 sandwich_3.1-1 labeling_0.4.3 S7_0.2.1
[21] spatstat.data_3.1-9 askpass_1.2.1 ggridges_0.5.7 pbapply_1.7-4
[25] R.utils_2.13.0 parallelly_1.45.1 maps_3.4.3 rstudioapi_0.17.1
[29] generics_0.1.4 shape_1.4.6.1 gtools_3.9.5 ica_1.0-3
[33] spatstat.random_3.4-3 zip_2.3.3 S4Vectors_0.42.1 abind_1.4-8
[37] R.methodsS3_1.8.2 lifecycle_1.0.4 yaml_2.3.10 SummarizedExperiment_1.34.0
[41] SparseArray_1.4.8 Rtsne_0.17 promises_1.5.0 gdata_3.0.1
[45] crayon_1.5.3 miniUI_0.1.2 lattice_0.22-7 scGate_1.7.2
[49] pillar_1.11.1 knitr_1.50 GenomicRanges_1.56.2 rjson_0.2.23
[53] boot_1.3-32 future.apply_1.20.0 codetools_0.2-20 glue_1.8.0
[57] spatstat.univar_3.1-5 data.table_1.17.8 vctrs_0.6.5 png_0.1-8
[61] spam_2.11-1 Rdpack_2.6.4 cellranger_1.1.0 gtable_0.3.6
[65] cachem_1.1.0 xfun_0.54 S4Arrays_1.4.1 rbibutils_2.3
[69] mime_0.13 tidygraph_1.3.1 pracma_2.4.4 reformulas_0.4.1
[73] rsconnect_1.5.1 SingleCellExperiment_1.26.0 iterators_1.0.14 fields_17.1
[77] statmod_1.5.1 fitdistrplus_1.2-4 ROCR_1.0-11 nlme_3.1-168
[81] bit64_4.6.0-1 RcppAnnoy_0.0.22 GenomeInfoDb_1.40.1 irlba_2.3.5.1
[85] vipor_0.4.7 KernSmooth_2.23-26 otel_0.2.0 colorspace_2.1-2
[89] BiocGenerics_0.50.0 STACAS_2.3.0 UCell_2.8.0 tidyselect_1.2.1
[93] bit_4.6.0 compiler_4.4.0 BiocNeighbors_1.22.0 hdf5r_1.3.12
[97] xml2_1.4.0 DelayedArray_0.30.1 plotly_4.11.0 lmtest_0.9-40
[101] digest_0.6.39 goftest_1.2-3 spatstat.utils_3.2-0 minqa_1.2.8
[105] rmarkdown_2.30 XVector_0.44.0 htmltools_0.5.8.1 pkgconfig_2.0.3
[109] umap_0.2.10.0 MatrixGenerics_1.16.0 fastmap_1.2.0 UCSC.utils_1.0.0
[113] rlang_1.1.6 GlobalOptions_0.1.2 htmlwidgets_1.6.4 shiny_1.11.1
[117] farver_2.1.2 zoo_1.8-14 jsonlite_2.0.0 BiocParallel_1.38.0
[121] R.oo_1.27.1 magrittr_2.0.4 GenomeInfoDbData_1.2.12 dotCall64_1.2
[125] Rcpp_1.1.0 viridis_0.6.5 reticulate_1.44.1 stringi_1.8.7
[129] zlibbioc_1.50.0 plyr_1.8.9 parallel_4.4.0 listenv_0.10.0
[133] deldir_2.0-4 graphlayouts_1.2.2 gridtext_0.1.5 tensor_1.5.1
[137] hms_1.1.4 circlize_0.4.16 igraph_2.2.1 spatstat.geom_3.6-1
[141] RcppHNSW_0.6.0 stats4_4.4.0 futile.options_1.0.1 evaluate_1.0.5
[145] lambda.r_1.2.4 nloptr_2.2.1 tzdb_0.5.0 tweenr_2.0.3
[149] httpuv_1.6.16 openssl_2.3.4 RANN_2.6.2 purrr_1.2.0
[153] polyclip_1.10-7 future_1.68.0 clue_0.3-66 scattermore_1.2
[157] xtable_1.8-4 RSpectra_0.16-2 later_1.4.4 viridisLite_0.4.2
[161] memoise_2.0.1 beeswarm_0.4.0 IRanges_2.38.1 cluster_2.1.8.1
[165] globals_0.18.0
`