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Plots not printing #185
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Hi @hcjarnagin, I think the issue is likely with your version of Nebulosa. Can you update to latest dev branch of scCustomize ("release/2.0.0") and then run Best, library(tidyverse)
library(Seurat)
#> Loading required package: SeuratObject
#> Loading required package: sp
#>
#> Attaching package: 'SeuratObject'
#> The following objects are masked from 'package:base':
#>
#> intersect, t
library(scCustomize)
#> scCustomize v2.1.2.9063
#> If you find the scCustomize useful please cite.
#> See 'samuel-marsh.github.io/scCustomize/articles/FAQ.html' for citation info.
pbmc <- pbmc3k.SeuratData::pbmc3k.final
pbmc <- suppressMessages(UpdateSeuratObject(pbmc))
#> Warning: Assay RNA changing from Assay to Assay
#> Warning: Graph RNA_nn changing from Graph to Graph
#> Warning: Graph RNA_snn changing from Graph to Graph
#> Warning: DimReduc pca changing from DimReduc to DimReduc
#> Warning: DimReduc umap changing from DimReduc to DimReduc
#> Warning: Adding a command log without an assay associated with it
#> Adding a command log without an assay associated with it
Plot_Density_Custom(pbmc, "CD14") Created on 2024-05-14 with reprex v2.1.0 Session infosessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.4.0 (2024-04-24)
#> os macOS Monterey 12.7.4
#> system x86_64, darwin20
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz America/New_York
#> date 2024-05-14
#> pandoc 3.1.11 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/x86_64/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> abind 1.4-5 2016-07-21 [1] CRAN (R 4.4.0)
#> beeswarm 0.4.0 2021-06-01 [1] CRAN (R 4.4.0)
#> Biobase 2.64.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
#> BiocGenerics 0.50.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
#> Cairo 1.6-2 2023-11-28 [1] CRAN (R 4.4.0)
#> circlize 0.4.16 2024-02-20 [1] CRAN (R 4.4.0)
#> cli 3.6.2 2023-12-11 [1] CRAN (R 4.4.0)
#> cluster 2.1.6 2023-12-01 [1] CRAN (R 4.4.0)
#> codetools 0.2-20 2024-03-31 [1] CRAN (R 4.4.0)
#> colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.4.0)
#> cowplot 1.1.3 2024-01-22 [1] CRAN (R 4.4.0)
#> crayon 1.5.2 2022-09-29 [1] CRAN (R 4.4.0)
#> curl 5.2.1 2024-03-01 [1] CRAN (R 4.4.0)
#> data.table 1.15.4 2024-03-30 [1] CRAN (R 4.4.0)
#> DelayedArray 0.30.1 2024-05-07 [1] Bioconductor 3.19 (R 4.4.0)
#> deldir 2.0-4 2024-02-28 [1] CRAN (R 4.4.0)
#> digest 0.6.35 2024-03-11 [1] CRAN (R 4.4.0)
#> dotCall64 1.1-1 2023-11-28 [1] CRAN (R 4.4.0)
#> dplyr * 1.1.4 2023-11-17 [1] CRAN (R 4.4.0)
#> evaluate 0.23 2023-11-01 [1] CRAN (R 4.4.0)
#> fansi 1.0.6 2023-12-08 [1] CRAN (R 4.4.0)
#> farver 2.1.2 2024-05-13 [1] CRAN (R 4.4.0)
#> fastDummies 1.7.3 2023-07-06 [1] CRAN (R 4.4.0)
#> fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.4.0)
#> fitdistrplus 1.1-11 2023-04-25 [1] CRAN (R 4.4.0)
#> forcats * 1.0.0 2023-01-29 [1] CRAN (R 4.4.0)
#> fs 1.6.4 2024-04-25 [1] CRAN (R 4.4.0)
#> future 1.33.2 2024-03-26 [1] CRAN (R 4.4.0)
#> future.apply 1.11.2 2024-03-28 [1] CRAN (R 4.4.0)
#> generics 0.1.3 2022-07-05 [1] CRAN (R 4.4.0)
#> GenomeInfoDb 1.40.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
#> GenomeInfoDbData 1.2.12 2024-05-01 [1] Bioconductor
#> GenomicRanges 1.56.0 2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
#> ggbeeswarm 0.7.2 2023-04-29 [1] CRAN (R 4.4.0)
#> ggplot2 * 3.5.1 2024-04-23 [1] CRAN (R 4.4.0)
#> ggprism 1.0.5 2024-03-21 [1] CRAN (R 4.4.0)
#> ggrastr 1.0.2 2023-06-01 [1] CRAN (R 4.4.0)
#> ggrepel 0.9.5 2024-01-10 [1] CRAN (R 4.4.0)
#> ggridges 0.5.6 2024-01-23 [1] CRAN (R 4.4.0)
#> GlobalOptions 0.1.2 2020-06-10 [1] CRAN (R 4.4.0)
#> globals 0.16.3 2024-03-08 [1] CRAN (R 4.4.0)
#> glue 1.7.0 2024-01-09 [1] CRAN (R 4.4.0)
#> goftest 1.2-3 2021-10-07 [1] CRAN (R 4.4.0)
#> gridExtra 2.3 2017-09-09 [1] CRAN (R 4.4.0)
#> gtable 0.3.5 2024-04-22 [1] CRAN (R 4.4.0)
#> highr 0.10 2022-12-22 [1] CRAN (R 4.4.0)
#> hms 1.1.3 2023-03-21 [1] CRAN (R 4.4.0)
#> htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0)
#> htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.4.0)
#> httpuv 1.6.15 2024-03-26 [1] CRAN (R 4.4.0)
#> httr 1.4.7 2023-08-15 [1] CRAN (R 4.4.0)
#> ica 1.0-3 2022-07-08 [1] CRAN (R 4.4.0)
#> igraph 2.0.3 2024-03-13 [1] CRAN (R 4.4.0)
#> IRanges 2.38.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
#> irlba 2.3.5.1 2022-10-03 [1] CRAN (R 4.4.0)
#> janitor 2.2.0 2023-02-02 [1] CRAN (R 4.4.0)
#> jsonlite 1.8.8 2023-12-04 [1] CRAN (R 4.4.0)
#> KernSmooth 2.23-22 2023-07-10 [1] CRAN (R 4.4.0)
#> knitr 1.46 2024-04-06 [1] CRAN (R 4.4.0)
#> ks 1.14.2 2024-01-15 [1] CRAN (R 4.4.0)
#> labeling 0.4.3 2023-08-29 [1] CRAN (R 4.4.0)
#> later 1.3.2 2023-12-06 [1] CRAN (R 4.4.0)
#> lattice 0.22-6 2024-03-20 [1] CRAN (R 4.4.0)
#> lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.4.0)
#> leiden 0.4.3.1 2023-11-17 [1] CRAN (R 4.4.0)
#> lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.4.0)
#> listenv 0.9.1 2024-01-29 [1] CRAN (R 4.4.0)
#> lmtest 0.9-40 2022-03-21 [1] CRAN (R 4.4.0)
#> lubridate * 1.9.3 2023-09-27 [1] CRAN (R 4.4.0)
#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.4.0)
#> MASS 7.3-60.2 2024-04-24 [1] local
#> Matrix 1.7-0 2024-03-22 [1] CRAN (R 4.4.0)
#> MatrixGenerics 1.16.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
#> matrixStats 1.3.0 2024-04-11 [1] CRAN (R 4.4.0)
#> mclust 6.1.1 2024-04-29 [1] CRAN (R 4.4.0)
#> mime 0.12 2021-09-28 [1] CRAN (R 4.4.0)
#> miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.4.0)
#> munsell 0.5.1 2024-04-01 [1] CRAN (R 4.4.0)
#> mvtnorm 1.2-4 2023-11-27 [1] CRAN (R 4.4.0)
#> Nebulosa 1.14.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
#> nlme 3.1-164 2023-11-27 [1] CRAN (R 4.4.0)
#> paletteer 1.6.0 2024-01-21 [1] CRAN (R 4.4.0)
#> parallelly 1.37.1 2024-02-29 [1] CRAN (R 4.4.0)
#> patchwork 1.2.0 2024-01-08 [1] CRAN (R 4.4.0)
#> pbapply 1.7-2 2023-06-27 [1] CRAN (R 4.4.0)
#> pbmc3k.SeuratData 3.1.4 2024-05-01 [1] local
#> pillar 1.9.0 2023-03-22 [1] CRAN (R 4.4.0)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.4.0)
#> plotly 4.10.4 2024-01-13 [1] CRAN (R 4.4.0)
#> plyr 1.8.9 2023-10-02 [1] CRAN (R 4.4.0)
#> png 0.1-8 2022-11-29 [1] CRAN (R 4.4.0)
#> polyclip 1.10-6 2023-09-27 [1] CRAN (R 4.4.0)
#> pracma 2.4.4 2023-11-10 [1] CRAN (R 4.4.0)
#> progressr 0.14.0 2023-08-10 [1] CRAN (R 4.4.0)
#> promises 1.3.0 2024-04-05 [1] CRAN (R 4.4.0)
#> purrr * 1.0.2 2023-08-10 [1] CRAN (R 4.4.0)
#> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.4.0)
#> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.4.0)
#> R.oo 1.26.0 2024-01-24 [1] CRAN (R 4.4.0)
#> R.utils 2.12.3 2023-11-18 [1] CRAN (R 4.4.0)
#> R6 2.5.1 2021-08-19 [1] CRAN (R 4.4.0)
#> RANN 2.6.1 2019-01-08 [1] CRAN (R 4.4.0)
#> RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.4.0)
#> Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.4.0)
#> RcppAnnoy 0.0.22 2024-01-23 [1] CRAN (R 4.4.0)
#> RcppHNSW 0.6.0 2024-02-04 [1] CRAN (R 4.4.0)
#> readr * 2.1.5 2024-01-10 [1] CRAN (R 4.4.0)
#> rematch2 2.1.2 2020-05-01 [1] CRAN (R 4.4.0)
#> reprex 2.1.0 2024-01-11 [1] CRAN (R 4.4.0)
#> reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.4.0)
#> reticulate 1.36.1 2024-04-22 [1] CRAN (R 4.4.0)
#> rlang 1.1.3 2024-01-10 [1] CRAN (R 4.4.0)
#> rmarkdown 2.26 2024-03-05 [1] CRAN (R 4.4.0)
#> ROCR 1.0-11 2020-05-02 [1] CRAN (R 4.4.0)
#> RSpectra 0.16-1 2022-04-24 [1] CRAN (R 4.4.0)
#> rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.4.0)
#> Rtsne 0.17 2023-12-07 [1] CRAN (R 4.4.0)
#> S4Arrays 1.4.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
#> S4Vectors 0.42.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
#> scales 1.3.0 2023-11-28 [1] CRAN (R 4.4.0)
#> scattermore 1.2 2023-06-12 [1] CRAN (R 4.4.0)
#> scCustomize * 2.1.2.9063 2024-05-10 [1] Github (samuel-marsh/scCustomize@e23ca06)
#> sctransform 0.4.1 2023-10-19 [1] CRAN (R 4.4.0)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.4.0)
#> Seurat * 5.1.0 2024-05-10 [1] CRAN (R 4.4.0)
#> SeuratObject * 5.0.2 2024-05-08 [1] CRAN (R 4.4.0)
#> shape 1.4.6.1 2024-02-23 [1] CRAN (R 4.4.0)
#> shiny 1.8.1.1 2024-04-02 [1] CRAN (R 4.4.0)
#> SingleCellExperiment 1.26.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
#> snakecase 0.11.1 2023-08-27 [1] CRAN (R 4.4.0)
#> sp * 2.1-4 2024-04-30 [1] CRAN (R 4.4.0)
#> spam 2.10-0 2023-10-23 [1] CRAN (R 4.4.0)
#> SparseArray 1.4.3 2024-05-07 [1] Bioconductor 3.19 (R 4.4.0)
#> spatstat.data 3.0-4 2024-01-15 [1] CRAN (R 4.4.0)
#> spatstat.explore 3.2-7 2024-03-21 [1] CRAN (R 4.4.0)
#> spatstat.geom 3.2-9 2024-02-28 [1] CRAN (R 4.4.0)
#> spatstat.random 3.2-3 2024-02-29 [1] CRAN (R 4.4.0)
#> spatstat.sparse 3.0-3 2023-10-24 [1] CRAN (R 4.4.0)
#> spatstat.utils 3.0-4 2023-10-24 [1] CRAN (R 4.4.0)
#> stringi 1.8.4 2024-05-06 [1] CRAN (R 4.4.0)
#> stringr * 1.5.1 2023-11-14 [1] CRAN (R 4.4.0)
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#> tidyr * 1.3.1 2024-01-24 [1] CRAN (R 4.4.0)
#> tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.4.0)
#> tidyverse * 2.0.0 2023-02-22 [1] CRAN (R 4.4.0)
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#> UCSC.utils 1.0.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
#> utf8 1.2.4 2023-10-22 [1] CRAN (R 4.4.0)
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#> vipor 0.4.7 2023-12-18 [1] CRAN (R 4.4.0)
#> viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.4.0)
#> withr 3.0.0 2024-01-16 [1] CRAN (R 4.4.0)
#> xfun 0.43 2024-03-25 [1] CRAN (R 4.4.0)
#> xml2 1.3.6 2023-12-04 [1] CRAN (R 4.4.0)
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#> XVector 0.44.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
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#> zlibbioc 1.50.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
#> zoo 1.8-12 2023-04-13 [1] CRAN (R 4.4.0)
#>
#> [1] /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library
#>
#> ────────────────────────────────────────────────────────────────────────────── |
Thank you so much for your suggestion! Reverting scCustomize back to 2.0.0 worked. I did have to download XQuartz to my computer and restart R to ensure Cairo was functional, after reverting this package. Thanks again for the great package and the helpful response! Seems to be fully functional now. |
All scCustomize/Nebulosa Plots are not printing to my R version. If I use ggplot2 versions > 3.4.4 I receive this error:
Error in
Plot_Density_Custom()
:! Due to error in Nebulosa package and ggplot2 v3.5.0 Plot_Density_Custom
functionality is currently restricted to ggplot v3.4.4 or lower.
If I use ggplot2 versions <= 3.4.4, the plots simply print to a blank screen. I can save them as an object and see the elements in the object lists, but can't print to a PDF, Tiff, or even make it visible.
Do you have any suggestions?
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