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pwwang / scplotter

scplotter is an R package that is built upon plotthis. It provides a set of functions to visualize single-cell sequencing data in an easy and efficient way.
https://pwwang.github.io/scplotter/
GNU General Public License v3.0
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ClonalResidencyPlot() - Error: 'venn_regionlabel' #1

Closed Hofphi closed 3 hours ago

Hofphi commented 3 hours ago

Hi,

thank you very much for this great tool. I am finally able to generate informative plots in a fast manner.

However, I have an issue related to ggVennDiagram when using ClonalResidencyPlot() with 'type=upset':

_Error: 'vennregionlabel' is not an exported object from 'namespace:ggVennDiagram' 

data(contig_list, package = "scRepertoire")
data <- scRepertoire::combineTCR(contig_list,
                                 samples = c("P17B", "P17L", "P18B", "P18L", "P19B","P19L", "P20B", "P20L")
                                 )
data <- scRepertoire::addVariable(data,
                                  variable.name = "Type",
                                  variables = rep(c("B", "L"), 4)
                                  )
data <- scRepertoire::addVariable(data,
                                  variable.name = "Subject",
                                  variables = rep(c("P17", "P18", "P19", "P20"), each = 2)
                                  )                         
ClonalResidencyPlot(data, plot_type = "upset", groups = c("P18B", "P18L"))
Error: 'venn_regionlabel' is not an exported object from 'namespace:ggVennDiagram'

I would very much appreciate your help.

Here is my session info: 

R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3 
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3;  LAPACK version 3.10.0

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

time zone: Europe/Berlin
tzcode source: system (glibc)

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

other attached packages:
[1] scplotter_0.1.0    dplyr_1.1.4        scRepertoire_2.0.8 ggplot2_3.5.1      Seurat_5.0.1       SeuratObject_5.0.0 sp_2.1-4          

loaded via a namespace (and not attached):
  [1] cubature_2.1.0              RcppAnnoy_0.0.22            splines_4.3.0               later_1.3.2                 bitops_1.0-7               
  [6] tibble_3.2.1                polyclip_1.10-6             janitor_2.2.0               fastDummies_1.7.3           lifecycle_1.0.4            
 [11] sf_1.0-6                    globals_0.16.3              lattice_0.22-5              MASS_7.3-60                 magrittr_2.0.3             
 [16] plotly_4.10.4               httpuv_1.6.15               sctransform_0.4.1           spam_2.10-0                 spatstat.sparse_3.0-3      
 [21] reticulate_1.37.0           DBI_1.1.3                   cowplot_1.1.3               pbapply_1.7-2               RColorBrewer_1.1-3         
 [26] lubridate_1.9.3             abind_1.4-5                 zlibbioc_1.48.0             BuenColors_0.5.6            Rtsne_0.17                 
 [31] GenomicRanges_1.54.1        purrr_1.0.2                 ggraph_2.1.0                BiocGenerics_0.48.1         RCurl_1.98-1.13            
 [36] hash_2.2.6.3                tweenr_2.0.2                evmix_2.12                  circlize_0.4.16             GenomeInfoDbData_1.2.11    
 [41] IRanges_2.36.0              S4Vectors_0.40.1            ggrepel_0.9.6               irlba_2.3.5.1               listenv_0.9.1              
 [46] spatstat.utils_3.0-4        units_0.8-4                 iNEXT_3.0.1                 MatrixModels_0.5-3          goftest_1.2-3              
 [51] RSpectra_0.16-1             spatstat.random_3.2-3       fitdistrplus_1.1-11         parallelly_1.37.1           leiden_0.4.3.1             
 [56] codetools_0.2-19            DelayedArray_0.28.0         scCustomize_2.0.0           xml2_1.3.6                  ggforce_0.4.1              
 [61] tidyselect_1.2.1            shape_1.4.6.1               farver_2.1.2                viridis_0.6.4               matrixStats_1.3.0          
 [66] stats4_4.3.0                spatstat.explore_3.2-7      jsonlite_1.8.8              e1071_1.7-14                tidygraph_1.2.3            
 [71] progressr_0.14.0            ggridges_0.5.6              ggalluvial_0.12.5           survival_3.5-7              ggnewscale_0.5.0           
 [76] tools_4.3.0                 stringdist_0.9.10           ica_1.0-3                   ggVennDiagram_1.2.3         Rcpp_1.0.13                
 [81] glue_1.8.0                  gridExtra_2.3               SparseArray_1.2.2           MatrixGenerics_1.14.0       GenomeInfoDb_1.38.1        
 [86] withr_3.0.1                 fastmap_1.2.0               fansi_1.0.6                 SparseM_1.81                digest_0.6.35              
 [91] timechange_0.2.0            R6_2.5.1                    mime_0.12                   ggprism_1.0.4               colorspace_2.1-1           
 [96] scattermore_1.2             tensor_1.5                  spatstat.data_3.0-4         utf8_1.2.4                  tidyr_1.3.1                
[101] generics_0.1.3              data.table_1.15.4           class_7.3-22                graphlayouts_1.0.2          httr_1.4.7                 
[106] htmlwidgets_1.6.4           S4Arrays_1.2.0              uwot_0.2.2                  pkgconfig_2.0.3             gtable_0.3.5               
[111] lmtest_0.9-40               SingleCellExperiment_1.24.0 XVector_0.42.0              htmltools_0.5.8.1           dotCall64_1.1-1            
[116] scales_1.3.0                Biobase_2.62.0              png_0.1-8                   snakecase_0.11.1            ggdendro_0.2.0             
[121] rstudioapi_0.15.0           rjson_0.2.21                reshape2_1.4.4              nlme_3.1-163                proxy_0.4-27               
[126] zoo_1.8-12                  GlobalOptions_0.1.2         stringr_1.5.1               RVenn_1.1.0                 KernSmooth_2.23-22         
[131] parallel_4.3.0              miniUI_0.1.1.1              vipor_0.4.5                 ggrastr_1.0.2               pillar_1.9.0               
[136] grid_4.3.0                  vctrs_0.6.5                 RANN_2.6.1                  VGAM_1.1-9                  promises_1.3.0             
[141] xtable_1.8-4                cluster_2.1.4               beeswarm_0.4.0              paletteer_1.5.0             truncdist_1.0-2            
[146] cli_3.6.3                   compiler_4.3.0              rlang_1.1.4                 crayon_1.5.2                future.apply_1.11.2        
[151] labeling_0.4.3              classInt_0.4-10             rematch2_2.1.2              plyr_1.8.9                  forcats_1.0.0              
[156] ggbeeswarm_0.7.2            stringi_1.8.4               viridisLite_0.4.2           deldir_2.0-4                assertthat_0.2.1           
[161] munsell_0.5.1               gsl_2.1-8                   lazyeval_0.2.2              spatstat.geom_3.2-9         quantreg_5.97              
[166] Matrix_1.6-3                RcppHNSW_0.6.0              patchwork_1.3.0             future_1.33.2               shiny_1.8.1.1              
[171] plotthis_0.3.2              SummarizedExperiment_1.32.0 evd_2.3-6.1                 ROCR_1.0-11                 gridtext_0.1.5             
[176] igraph_2.0.3
pwwang commented 2 hours ago

What's going on here?

Hofphi commented 2 hours ago

I had installed an older version of ggVennDiagram which caused the faulty behavior during ClonalResidencyPlot().

I closed the issue once I have realized that.

Sorry for the confusion.