setting combine = FALSE in FeaturePlot_scCustomize() returns NULL · Issue #31 · samuel-marsh/scCustomize (original) (raw)
There seems to be a problem when the combine = FALSE flag is set in FeaturePlot_scCustomize(). The function call simply returns NULL. Find mwe below, thanks a lot for your help!
Best, Niko
library(Seurat)
library(SeuratData)
library(scCustomize)
library(dplyr)
InstallData("pbmc3k")
data("pbmc3k")
pbmc = pbmc3k %>%
NormalizeData() %>%
ScaleData() %>%
FindVariableFeatures() %>%
RunPCA() %>%
RunUMAP(dims = 1:10)
FeaturePlot(pbmc,features = c('NRG1','ERBB2'), combine = FALSE)
FeaturePlot_scCustom(pbmc,features = c('NRG1','ERBB2'), combine = FALSE)
Output:
[[1]]
[[2]]
NULL
SessionInfo:
R version 4.1.2 (2021-11-01)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.2.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] pbmc3k.SeuratData_3.1.4 scCustomize_0.7.0 SeuratData_0.2.1 SeuratObject_4.0.4 Seurat_4.1.0
[6] dplyr_1.0.8
loaded via a namespace (and not attached):
[1] utf8_1.2.2 reticulate_1.24 tidyselect_1.1.2 htmlwidgets_1.5.4
[5] grid_4.1.2 Rtsne_0.15 devtools_2.4.3 munsell_0.5.0
[9] codetools_0.2-18 ica_1.0-2 future_1.24.0 miniUI_0.1.1.1
[13] withr_2.5.0 spatstat.random_2.2-0 colorspace_2.0-3 Biobase_2.54.0
[17] rstudioapi_0.13 stats4_4.1.2 SingleCellExperiment_1.16.0 ROCR_1.0-11
[21] ggsignif_0.6.3 tensor_1.5 listenv_0.8.0 labeling_0.4.2
[25] MatrixGenerics_1.6.0 GenomeInfoDbData_1.2.7 polyclip_1.10-0 farver_2.1.0
[29] pheatmap_1.0.12 rprojroot_2.0.3 parallelly_1.30.0 vctrs_0.4.0
[33] generics_0.1.2 dittoSeq_1.7.0 R6_2.5.1 GenomeInfoDb_1.30.1
[37] ggbeeswarm_0.6.0 bitops_1.0-7 spatstat.utils_2.3-0 cachem_1.0.6
[41] DelayedArray_0.20.0 promises_1.2.0.1 scales_1.1.1 beeswarm_0.4.0
[45] gtable_0.3.0 globals_0.14.0 processx_3.5.3 goftest_1.2-3
[49] rlang_1.0.2 GlobalOptions_0.1.2 splines_4.1.2 rstatix_0.7.0
[53] lazyeval_0.2.2 spatstat.geom_2.4-0 broom_0.7.12 reshape2_1.4.4
[57] abind_1.4-5 backports_1.4.1 httpuv_1.6.5 tools_4.1.2
[61] usethis_2.1.5 ggplot2_3.3.5 ellipsis_0.3.2 spatstat.core_2.4-2
[65] RColorBrewer_1.1-3 BiocGenerics_0.40.0 sessioninfo_1.2.2 ggridges_0.5.3
[69] Rcpp_1.0.8.3 plyr_1.8.7 zlibbioc_1.40.0 purrr_0.3.4
[73] RCurl_1.98-1.6 ps_1.6.0 prettyunits_1.1.1 ggpubr_0.4.0
[77] rpart_4.1.16 deldir_1.0-6 pbapply_1.5-0 viridis_0.6.2
[81] cowplot_1.1.1 S4Vectors_0.32.4 zoo_1.8-9 SummarizedExperiment_1.24.0
[85] ggrepel_0.9.1 cluster_2.1.2 fs_1.5.2 magrittr_2.0.3
[89] RSpectra_0.16-0 data.table_1.14.2 scattermore_0.8 circlize_0.4.14
[93] lmtest_0.9-40 RANN_2.6.1 fitdistrplus_1.1-8 matrixStats_0.61.0
[97] pkgload_1.2.4 patchwork_1.1.1 mime_0.12 xtable_1.8-4
[101] IRanges_2.28.0 gridExtra_2.3 shape_1.4.6 testthat_3.1.3
[105] compiler_4.1.2 tibble_3.1.6 colorway_0.2.0 KernSmooth_2.23-20
[109] crayon_1.5.1 htmltools_0.5.2 mgcv_1.8-39 later_1.3.0
[113] ggprism_1.0.3.9000 tidyr_1.2.0 lubridate_1.8.0 MASS_7.3-55
[117] rappdirs_0.3.3 Matrix_1.4-0 car_3.0-12 brio_1.1.3
[121] cli_3.2.0 parallel_4.1.2 igraph_1.3.0 GenomicRanges_1.46.1
[125] forcats_0.5.1 pkgconfig_2.0.3 plotly_4.10.0 spatstat.sparse_2.1-0
[129] paletteer_1.4.0 vipor_0.4.5 XVector_0.34.0 snakecase_0.11.0
[133] stringr_1.4.0 callr_3.7.0 digest_0.6.29 sctransform_0.3.3
[137] RcppAnnoy_0.0.19 janitor_2.1.0 spatstat.data_2.1-4 leiden_0.3.9
[141] uwot_0.1.11 curl_4.3.2 shiny_1.7.1 lifecycle_1.0.1
[145] nlme_3.1-155 jsonlite_1.8.0 carData_3.0-5 desc_1.4.1
[149] viridisLite_0.4.0 fansi_1.0.3 pillar_1.7.0 lattice_0.20-45
[153] fastmap_1.1.0 httr_1.4.2 pkgbuild_1.3.1 survival_3.3-1
[157] glue_1.6.2 remotes_2.4.2 png_0.1-7 stringi_1.7.6
[161] rematch2_2.1.2 memoise_2.0.1 renv_0.15.4 irlba_2.3.5
[165] future.apply_1.8.1