Include Missing Intersections

[drneavin]

Hi @krassowski,

I would like the ability to include intersections that have no counts in it for easy comparison between certain upset plots that I am creating. I'm wondering if there is already a mechanism to do this?

I have tried min_size=0 and specifying the intersections that I want to plot with intersections=list(...) but can't seem to get it to plot the intersections without any counts. Is this possible?

I am using ComplexUpset version 1.1.0

My R.Version() output is:

$platform
[1] "x86_64-conda-linux-gnu"

$arch
[1] "x86_64"

$os
[1] "linux-gnu"

$system
[1] "x86_64, linux-gnu"

$status
[1] ""

$major
[1] "4"

$minor
[1] "0.3"

$year
[1] "2020"

$month
[1] "10"

$day
[1] "10"

$`svn rev`
[1] "79318"

$language
[1] "R"

$version.string
[1] "R version 4.0.3 (2020-10-10)"

$nickname
[1] "Bunny-Wunnies Freak Out"

My sessionInfo() output is:

 version 4.0.3 (2020-10-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /path/anaconda3/envs/baseR402/lib/libblas.so.3.8.0
LAPACK: /path/anaconda3/envs/baseR402/lib/liblapack.so.3.8.0

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

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

other attached packages:
 [1] plyr_1.8.6           RColorBrewer_1.1-2   ComplexUpset_1.1.0  
 [4] ggforce_0.3.2        ggnewscale_0.4.5     viridis_0.5.1       
 [7] viridisLite_0.3.0    ggpubr_0.4.0         circlize_0.4.12     
[10] awtools_0.2.1        ComplexHeatmap_2.6.2 forcats_0.5.1       
[13] stringr_1.4.0        dplyr_1.0.4          purrr_0.3.4         
[16] readr_1.4.0          tibble_3.1.0         ggplot2_3.3.3       
[19] tidyverse_1.3.0      tidyr_1.1.2          SeuratObject_4.0.0  
[22] Seurat_4.0.0        

loaded via a namespace (and not attached):
  [1] readxl_1.3.1         backports_1.2.1      igraph_1.2.6        
  [4] lazyeval_0.2.2       splines_4.0.3        listenv_0.8.0       
  [7] scattermore_0.7      digest_0.6.27        htmltools_0.5.1.1   
 [10] fansi_0.4.2          magrittr_2.0.1       tensor_1.5          
 [13] cluster_2.1.1        ROCR_1.0-11          openxlsx_4.2.3      
 [16] globals_0.14.0       modelr_0.1.8         matrixStats_0.58.0  
 [19] colorspace_2.0-0     rvest_0.3.6          ggrepel_0.9.1       
 [22] haven_2.3.1          crayon_1.4.1         jsonlite_1.7.2      
 [25] spatstat_1.64-1      spatstat.data_2.0-0  survival_3.2-7      
 [28] zoo_1.8-8            glue_1.4.2           polyclip_1.10-0     
 [31] gtable_0.3.0         leiden_0.3.7         GetoptLong_1.0.5    
 [34] car_3.0-10           future.apply_1.7.0   shape_1.4.5         
 [37] BiocGenerics_0.36.0  abind_1.4-5          scales_1.1.1        
 [40] DBI_1.1.1            rstatix_0.7.0        miniUI_0.1.1.1      
 [43] Rcpp_1.0.6           xtable_1.8-4         clue_0.3-58         
 [46] reticulate_1.18      foreign_0.8-81       stats4_4.0.3        
 [49] htmlwidgets_1.5.3    httr_1.4.2           ellipsis_0.3.1      
 [52] ica_1.0-2            farver_2.1.0         pkgconfig_2.0.3     
 [55] uwot_0.1.10          dbplyr_2.1.0         deldir_0.2-10       
 [58] utf8_1.1.4           labeling_0.4.2       tidyselect_1.1.0    
 [61] rlang_0.4.10         reshape2_1.4.4       later_1.1.0.1       
 [64] munsell_0.5.0        cellranger_1.1.0     tools_4.0.3         
 [67] cli_2.3.1            generics_0.1.0       broom_0.7.5         
 [70] ggridges_0.5.3       fastmap_1.1.0        goftest_1.2-2       
 [73] fs_1.5.0             fitdistrplus_1.1-3   zip_2.1.1           
 [76] RANN_2.6.1           pbapply_1.4-3        future_1.21.0       
 [79] nlme_3.1-152         mime_0.10            xml2_1.3.2          
 [82] compiler_4.0.3       rstudioapi_0.13      plotly_4.9.3        
 [85] curl_4.3             png_0.1-7            ggsignif_0.6.1      
 [88] spatstat.utils_2.0-0 reprex_1.0.0         tweenr_1.0.1        
 [91] stringi_1.5.3        ps_1.6.0             lattice_0.20-41     
 [94] Matrix_1.3-2         vctrs_0.3.6          pillar_1.5.1        
 [97] lifecycle_1.0.0      lmtest_0.9-38        GlobalOptions_0.1.2 
[100] RcppAnnoy_0.0.18     data.table_1.14.0    cowplot_1.1.1       
[103] irlba_2.3.3          httpuv_1.5.5         patchwork_1.1.1     
[106] R6_2.5.0             promises_1.2.0.1     KernSmooth_2.23-18  
[109] gridExtra_2.3        rio_0.5.26           IRanges_2.23.10     
[112] parallelly_1.23.0    codetools_0.2-18     MASS_7.3-53         
[115] assertthat_0.2.1     rjson_0.2.20         withr_2.4.1         
[118] sctransform_0.3.2    S4Vectors_0.28.1     mgcv_1.8-34         
[121] parallel_4.0.3       hms_1.0.0            rpart_4.1-15        
[124] carData_3.0-4        Cairo_1.5-12.2       Rtsne_0.15          
[127] shiny_1.6.0          lubridate_1.7.10    

Thanks for your help!

[krassowski]

Thank you for this suggestion. Do I understand correctly that this is the same issue as in #99?
If yes then it is not possible in 1.1, but I plan to make it possible in the next version (1.2).

[drneavin]

Hi @krassowski ,

Yes, you are right that it is the same enhancement suggestion as #99 - sorry to put in a duplicated issue. I'll look forward to the next version to try out this additional functionality. Thanks for responding so quickly!

[krassowski]

Hi @drneavin,

This is now possible - please see #99 (comment) and let me know if it works well for you.