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View Code? Open in Web Editor NEWVenn diagrams with directionality (concordance), optional display of items inside the figure, text Venn diagrams
Home Page: https://jmw86069.github.io/venndir
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could not find function "tcount"
Hello,
I followed the installation instruction and test as in the README, I hit an error, please advise, thank you!
library(venndir)
setlist <- make_venn_test(100, 3)
venndir(setlist)
Error in tcount(sign(diff(h1h2df1$h2))) :
could not find function "tcount"
setlist
$set_A
[1] "item_067" "item_042" "item_050" "item_043" "item_014" "item_025"
[7] "item_090" "item_091" "item_069" "item_093" "item_057" "item_009"
[13] "item_072" "item_026" "item_007" "item_099" "item_089" "item_083"
[19] "item_036" "item_078" "item_097" "item_076" "item_015" "item_032"
[25] "item_086" "item_084" "item_041" "item_023" "item_027" "item_060"
[31] "item_053" "item_079"
$set_B
[1] "item_053" "item_027" "item_096" "item_038" "item_089" "item_034"
[7] "item_093" "item_069" "item_072" "item_076" "item_063" "item_013"
[13] "item_082" "item_025" "item_097" "item_021"
$set_C
[1] "item_079" "item_041" "item_047" "item_090" "item_060" "item_095"
[7] "item_016" "item_006" "item_072" "item_086" "item_091" "item_039"
[13] "item_031" "item_081" "item_050"
venndir(setlist)
Error in tcount(sign(diff(h1h2df1$h2))) :
could not find function "tcount"
sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.so
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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] venndir_0.0.17.9000 remotes_2.4.0
loaded via a namespace (and not attached):
[1] lattice_0.20-44 ps_1.6.0 prettyunits_1.1.1
[4] crayon_1.4.1 withr_2.4.2 rprojroot_2.0.2
[7] grid_4.1.0 R6_2.5.0 cli_3.0.0
[10] curl_4.3.2 data.table_1.14.0 rstudioapi_0.13
[13] sp_1.4-5 callr_3.7.0 jamba_0.0.70.900
[16] tools_4.1.0 colorjam_0.0.22.900 compiler_4.1.0
[19] processx_3.5.2 pkgbuild_1.2.0
Migrate from sp/rgeos to polyclip
The latest update to the sp and rgeos R packages did in fact remove rgeos from CRAN. Despite a year advance warning, it was not easy to perform a drop-in replacement with the sf package, in part because until recently our linux system was unable to install sf and its myriad dependencies. Something about requiring C++ newer than was available, then something about stdclib needing to be more recent, etc. etc.
The conclusion was to use polyclip instead of sf to fill the same roles: buffer outside/inside a given polygon; distance from point to polygon, nearest polygon, things like that. These functions are available in polyclip and do not require installation of extensive geographic mapping libraries (as with sp and now sf). Also, polyclip is available on older versions of linux.
The task is to migrate venndir functions to use polyclip, thus removing all dependency on sp and rgeos.
No Labels/Text on Venn Diagram
For some reason the labels/text are all missing for the venn diagram. Not sure what is happening. I never managed to get them to show up. The only thing I can think of is: Warning: font family not found in Windows font database
setlist <- make_venn_test(2500, 3,
sizes=c(400, 500, 200),
do_signed=TRUE)
venndir(setlist, overlap_type="agreement", proportional=TRUE)
setlist <- make_venn_test(2500, 3,
sizes=c(400, 500, 200),
do_signed=TRUE)
venndir(setlist)
R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22621)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C LC_TIME=English_United States.utf8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] grid stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] farver_2.1.1 colorspace_2.1-0 readr_2.1.5 tximport_1.30.0
[5] org.Mm.eg.db_3.18.0 ensembldb_2.26.0 AnnotationFilter_1.26.0 GenomicFeatures_1.54.1
[9] AnnotationDbi_1.64.1 AnnotationHub_3.10.0 BiocFileCache_2.10.1 dbplyr_2.4.0
[13] venndir_0.0.29.900 GOplot_1.0.2 gridExtra_2.3 scales_1.3.0
[17] ggsci_3.0.0 kableExtra_1.3.4.9000 dendextend_1.17.1 ggdendro_0.1.23
[21] eulerr_7.0.0 ComplexHeatmap_2.18.0 EnhancedVolcano_1.20.0 ggrepel_0.9.4
[25] pheatmap_1.0.12 enrichplot_1.22.0 bigPint_1.19.1 vsn_3.70.0
[29] clusterProfiler_4.10.0 DESeq2_1.42.0 SummarizedExperiment_1.32.0 Biobase_2.62.0
[33] MatrixGenerics_1.14.0 matrixStats_1.2.0 GenomicRanges_1.54.1 GenomeInfoDb_1.38.5
[37] IRanges_2.36.0 S4Vectors_0.40.2 BiocGenerics_0.48.1 RColorBrewer_1.1-3
[41] ggtree_3.10.0 ggfortify_0.4.16 ggplot2_3.4.4 tibble_3.2.1
[45] dplyr_1.1.4
loaded via a namespace (and not attached):
[1] ProtGenerics_1.34.0 fs_1.6.3 bitops_1.0-7 sf_1.0-15
[5] HDO.db_0.99.1 httr_1.4.7 webshot_0.5.5 doParallel_1.0.17
[9] colorjam_0.0.27.900 tools_4.3.2 backports_1.4.1 utf8_1.2.4
[13] R6_2.5.1 lazyeval_0.2.2 GetoptLong_1.0.5 withr_3.0.0
[17] sp_1.6-1 prettyunits_1.2.0 GGally_2.2.0 preprocessCore_1.64.0
[21] cli_3.6.2 scatterpie_0.2.1 proxy_0.4-27 commonmark_1.9.0
[25] Rsamtools_2.18.0 systemfonts_1.0.5 yulab.utils_0.1.3 gson_0.1.0
[29] foreign_0.8-86 DOSE_3.28.2 svglite_2.1.3 limma_3.58.1
[33] rstudioapi_0.15.0 RSQLite_2.3.4 generics_0.1.3 gridGraphics_0.5-1
[37] shape_1.4.6 BiocIO_1.12.0 GO.db_3.18.0 Matrix_1.6-5
[41] fansi_1.0.6 abind_1.4-5 lifecycle_1.0.4 yaml_2.3.8
[45] qvalue_2.34.0 SparseArray_1.2.3 blob_1.2.4 promises_1.2.1
[49] crayon_1.5.2 shinydashboard_0.7.2 lattice_0.22-5 cowplot_1.1.2
[53] KEGGREST_1.42.0 pillar_1.9.0 knitr_1.45 fgsea_1.28.0
[57] rjson_0.2.21 codetools_0.2-19 fastmatch_1.1-4 glue_1.6.2
[61] ggfun_0.1.3 data.table_1.14.10 vctrs_0.6.5 png_0.1-8
[65] treeio_1.26.0 gtable_0.3.4 cachem_1.0.8 xfun_0.41
[69] S4Arrays_1.2.0 mime_0.12 tidygraph_1.3.0 iterators_1.0.14
[73] units_0.8-5 statmod_1.5.0 interactiveDisplayBase_1.40.0 ellipsis_0.3.2
[77] nlme_3.1-164 bit64_4.0.5 progress_1.2.3 filelock_1.0.3
[81] affyio_1.72.0 KernSmooth_2.23-22 rpart_4.1.23 DBI_1.2.1
[85] rgeos_0.6-4 Hmisc_5.1-1 nnet_7.3-19 tidyselect_1.2.0
[89] bit_4.0.5 compiler_4.3.2 curl_5.2.0 rvest_1.0.3
[93] htmlTable_2.4.2 xml2_1.3.6 DelayedArray_0.28.0 plotly_4.10.4
[97] shadowtext_0.1.2 rtracklayer_1.62.0 checkmate_2.3.1 classInt_0.4-10
[101] hexbin_1.28.3 affy_1.80.0 rappdirs_0.3.3 stringr_1.5.1
[105] digest_0.6.33 rmarkdown_2.25 XVector_0.42.0 htmltools_0.5.7
[109] pkgconfig_2.0.3 base64enc_0.1-3 fastmap_1.1.1 rlang_1.1.2
[113] GlobalOptions_0.1.2 htmlwidgets_1.6.4 shiny_1.8.0 jsonlite_1.8.8
[117] BiocParallel_1.36.0 GOSemSim_2.28.0 RCurl_1.98-1.13 magrittr_2.0.3
[121] Formula_1.2-5 GenomeInfoDbData_1.2.11 ggplotify_0.1.2 jamba_0.0.98.900
[125] patchwork_1.2.0 munsell_0.5.0 Rcpp_1.0.11 ape_5.7-1
[129] shinycssloaders_1.0.0 viridis_0.6.4 stringi_1.8.3 ggraph_2.1.0
[133] zlibbioc_1.48.0 MASS_7.3-60.0.1 plyr_1.8.9 ggstats_0.5.1
[137] parallel_4.3.2 Biostrings_2.70.1 graphlayouts_1.0.2 splines_4.3.2
[141] gridtext_0.1.5 hms_1.1.3 circlize_0.4.15 polylabelr_0.2.0
[145] locfit_1.5-9.8 igraph_1.6.0 markdown_1.12 reshape2_1.4.4
[149] biomaRt_2.58.0 BiocVersion_3.18.1 XML_3.99-0.16 evaluate_0.23
[153] BiocManager_1.30.22 tzdb_0.4.0 foreach_1.5.2 tweenr_2.0.2
[157] httpuv_1.6.13 tidyr_1.3.0 purrr_1.0.2 polyclip_1.10-6
[161] reshape_0.8.9 clue_0.3-65 gridBase_0.4-7 ggforce_0.4.1
[165] xtable_1.8-4 restfulr_0.0.15 e1071_1.7-14 tidytree_0.4.6
[169] later_1.3.2 class_7.3-22 viridisLite_0.4.2 aplot_0.2.2
[173] GenomicAlignments_1.38.0 memoise_2.0.1 cluster_2.1.6
Error in explodePolygons(x, ...) : use sf or terra functions)
Hi James,
I'm running into an error when running the example code. Code and session info pasted below. I was hoping you could identify if this is a dependency or other issue. The venndir package appears ideal for what I want to do so it would be great if I could get it working.
Many thanks,
Andrew
--- Code
library(venndir)
Registered S3 method overwritten by 'data.table':
method from
print.data.table
rgeos version: 0.6-4, (SVN revision 699)
GEOS runtime version: 3.8.3-CAPI-1.13.4
Please note that rgeos will be retired during October 2023,
plan transition to sf or terra functions using GEOS at your earliest convenience.
See https://r-spatial.org/r/2023/05/15/evolution4.html for details.
Linking to sp version: 2.1-1
Polygon checking: TRUE
options("warn"=-1)
setlist <- make_venn_test(100, 3)
venndir(setlist)
Error in explodePolygons(x, ...) : use sf or terra functions)
--- sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /bi/apps/R/4.1.1/lib64/R/lib/libRblas.so
LAPACK: /bi/apps/R/4.1.1/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 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 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] farver_2.1.1 matrixStats_1.0.0 colorspace_2.1-0 venndir_0.0.29.900
loaded via a namespace (and not attached):
[1] lattice_0.20-45 digest_0.6.33 grid_4.1.1 evaluate_0.22 rlang_1.1.1
[6] cli_3.6.1 data.table_1.14.8 rstudioapi_0.14 sp_2.1-1 jamba_0.0.96.900
[11] rmarkdown_2.25 tools_4.1.1 colorjam_0.0.27.900 xfun_0.40 yaml_2.3.7
[16] fastmap_1.1.1 compiler_4.1.1 rgeos_0.6-4 htmltools_0.5.6 knitr_1.44
options to avoid printing labels not working
Hi James
I tried to print a 7-lists venn plot. Very nice plot but I need to manually customize the labels with %ages instead of items. I tried to set options about labels and sets printing to "off"
e.g. venndir(setlist, proportional = TRUE, show_items = "none", show_label = "none", display_counts = FALSE,return_items = FALSE , show_set = "none" )
but the picture is still full of contents, as such:
May you check the code please? I tried to wotk on label_df object in the function but unsuccesfully
Many thanks
Luca
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