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Accelerating ggplot2
https://ggforce.data-imaginist.com
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geom_mark_hull does not work for some data points #290

Closed zhanghao-njmu closed 9 months ago

zhanghao-njmu commented 1 year ago

The following data and code can reproduce this issue. Note that the latest ggplot2 and ggforce are used.

library(ggplot2)
library(ggforce)
x <- c(-4.46798966620377, -2.1090312453605, -1.84601768294516, 5.79499827429486, 0.43592398267521, -3.01641689187153, -4.10398493436269, -1.53467832497444, -1.64403248330696, 1.88866969350521, -1.10071376022678, -0.732424476000914, 4.9355457310868, 7.16901087881661, -11.1749760466164, -0.330647142722807, 4.99431746262638, 3.99350248184654, 5.57024373532071, -4.9003441612954, -2.70964164932524, -3.13827001445066, 8.98938301829994, 1.15304888846147, -4.10835606970075, -3.80814439783665, -1.11500667144161, -4.01741501531724, 0.600033270173348, -1.80874358837064, -0.381658708050097, 6.46574124184736, 6.37340082097916, 0.273747698054138, 4.90249513991362, 6.16139025975088, 2.62462429559324, 5.36868924362433, -6.21295925665591, -2.27676433338093, -1.23143424193455, 5.79794917170878, 1.39159889636088, -3.27991565841227, -3.32113773742275, -1.89630876814511, -3.93776678590554, 0.785189427950814, -0.794902846480633, -0.628082507785516, 5.74575717936985, 7.04070961795171, 0.788392068682478, 5.60989643609462, 4.22291712058141, 2.10055019294984, 5.85725439334508)
y <- c(-1.88979052125517, -3.99859032133039, 2.88794711532744, 1.04400982509528, -9.20071736934793, -0.874436876290539, -5.01035759345655, 1.56129515932716, -2.28617788003896, 1.46927851645699, -1.23088074711093, -0.0512634990258398, 0.855694107232475, 5.24359789459775, -5.19349234505035, -5.80406825757198, 2.0373710339048, 3.66304250612958, 2.47355081727165, -2.91698101544892, -3.68956634231607, 5.84439063122804, 0.596732520647421, -8.31179169039804, -0.63493227634592, -5.93821117884396, 1.019956220117, -3.25066580239872, 1.34229087097502, -1.24120130291848, 1.55903028956034, 2.09890123632997, 4.16912629275164, -7.18715263054722, 3.06941990106059, 3.14300986520884, 3.17857513049073, 4.73226062353877, -3.44527637667008, -3.41082697427231, 3.63529860825317, 1.63130316772536, -9.30339326171906, -0.196903044477533, -5.23904552721807, 0.814520292592067, -2.58187687963695, 0.83932864039429, -1.73754258868063, 0.524089051459452, 0.100885472398243, 4.28702335064132, -5.19405687460876, 3.27950050157283, 2.34740358671191, 3.9834926184684, 5.45626038770104)
celltype <- c("Amnion", "Endoderm", "Endothelial & erythroid cell", "Ependymal cell", "Epiblast", "Epithelium", "ExE endoderm", "ExE mesoderm", "Gut", "Limb bud mesenchyme cell", "Mesoderm", "MSC/Fib", "Neural ectoderm", "Neuron", "PGC", "Primitive streak", "Radial glial cell", "Retinal pigmented epithelium", "Retinal progenitor cell", "Amnion & PGC", "Endoderm", "Endothelial & erythroid cell", "Ependymal cell", "Epiblast", "Epithelium", "ExE endoderm", "ExE mesoderm", "Gut", "Limb bud mesenchyme cell", "Mesoderm", "MSC/Fib", "Neural ectoderm", "Neuron", "Primitive streak", "Radial glial cell", "Retinal progenitor cell", "Schwann cell", "Sensory neuron", "Amnion & PGC", "Endoderm", "Endothelial & erythroid cell", "Ependymal cell", "Epiblast", "Epithelium", "ExE endoderm", "ExE mesoderm", "Gut", "Limb bud mesenchyme cell", "Mesoderm", "MSC/Fib", "Neural ectoderm", "Neuron", "Primitive streak", "Radial glial cell", "Retinal progenitor cell & RPE", "Schwann cell", "Sensory neuron")

When plotting with all the data above, geom_mark_hull only works for certain points.

df <- data.frame(x = x, y = y, celltype = celltype)
ggplot(data = df, aes(x, y)) +
  geom_point(mapping = aes(color = celltype)) +
  geom_mark_hull(mapping = aes(fill = celltype))

image

However, when plotting with a subset of data (<40 data points), geom_mark_hull works without any omissions.

ggplot(data = df[1:39,], aes(x, y)) +
  geom_point(mapping = aes(color = celltype)) +
  geom_mark_hull(mapping = aes(fill = celltype))

image

R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 8

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.12.so

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

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

other attached packages:
 [1] concaveman_1.1.0      ggforce_0.4.1         ggraph_2.1.0          igraph_1.3.5          RcppParallel_5.1.5    SCP_0.2.5.9010        openxlsx_4.2.5       
 [8] plotly_4.10.1         scales_1.2.1          circlize_0.4.15       ComplexHeatmap_2.15.1 stringr_1.5.0         UCell_2.0.1           dplyr_1.0.10         
[15] cowplot_1.1.1         ggplot2_3.4.0         SeuratDisk_0.0.0.9019 SeuratObject_4.1.3    Seurat_4.3.0         

loaded via a namespace (and not attached):
  [1] vcd_1.4-10                  ica_1.0-3                   class_7.3-20                V8_4.2.1                    foreach_1.5.2               lmtest_0.9-40              
  [7] rprojroot_2.0.3             crayon_1.5.2                laeken_0.5.2                MASS_7.3-58.1               Matrix.utils_0.9.8          nlme_3.1-160               
 [13] rlang_1.0.6                 XVector_0.38.0              ROCR_1.0-11                 irlba_2.3.5.1               limma_3.52.4                smoother_1.1               
 [19] filelock_1.0.2              BiocParallel_1.32.4         rjson_0.2.21                bit64_4.0.5                 glue_1.6.2                  sctransform_0.3.5          
 [25] parallel_4.2.0              spatstat.sparse_3.0-0       AnnotationDbi_1.60.0        BiocGenerics_0.44.0         classInt_0.4-8              yaImpute_1.0-33            
 [31] spatstat.geom_3.0-3         tidyselect_1.2.0            SummarizedExperiment_1.28.0 fitdistrplus_1.1-8          XML_3.99-0.13               tidyr_1.2.1                
 [37] zoo_1.8-11                  sf_1.0-9                    xtable_1.8-4                RcppHNSW_0.4.1              magrittr_2.0.3              cli_3.4.1                  
 [43] zlibbioc_1.44.0             rstudioapi_0.14             miniUI_0.1.1.1              sp_1.5-1                    parallelDist_0.2.6          RcppEigen_0.3.3.9.3        
 [49] shiny_1.7.4                 clue_0.3-63                 cluster_2.1.4               tidygraph_1.2.2             pcaMethods_1.88.0           KEGGREST_1.38.0            
 [55] tibble_3.1.8                ggrepel_0.9.2               listenv_0.9.0               Biostrings_2.66.0           png_0.1-8                   future_1.30.0              
 [61] withr_2.5.0                 bitops_1.0-7                ranger_0.14.1               plyr_1.8.8                  e1071_1.7-12                pillar_1.8.1               
 [67] GlobalOptions_0.1.2         cachem_1.0.6                scatterplot3d_0.3-42        hdf5r_1.3.7                 TTR_0.24.3                  GetoptLong_1.0.5           
 [73] xts_0.12.1                  vctrs_0.5.1                 ellipsis_0.3.2              generics_0.1.3              rgdal_1.5-32                tools_4.2.0                
 [79] munsell_0.5.0               tweenr_2.0.2                proxy_0.4-27                DelayedArray_0.24.0         fastmap_1.1.0               compiler_4.2.0             
 [85] abind_1.4-5                 httpuv_1.6.7                sessioninfo_1.2.2           rgeos_0.5-9                 GenomeInfoDbData_1.2.9      gridExtra_2.3              
 [91] lattice_0.20-45             ggnewscale_0.4.8            deldir_1.0-6                utf8_1.2.2                  later_1.3.0                 BiocFileCache_2.6.0        
 [97] jsonlite_1.8.4              ggplot.multistats_1.0.0     princurve_2.1.6             pbapply_1.6-0               carData_3.0-5               lazyeval_0.2.2             
[103] promises_1.2.0.1            car_3.1-0                   doParallel_1.0.17           R.utils_2.12.2              goftest_1.2-3               spatstat.utils_3.0-1       
[109] reticulate_1.26             Rtsne_0.16                  Biobase_2.58.0              uwot_0.1.14                 proxyC_0.3.3                yaml_2.3.6                 
[115] survival_3.4-0              systemfonts_1.0.4           htmltools_0.5.4             memoise_2.0.1               graphlayouts_0.8.4          IRanges_2.32.0             
[121] destiny_3.10.0              viridisLite_0.4.1           digest_0.6.31               assertthat_0.2.1            mime_0.12                   rappdirs_0.3.3             
[127] units_0.8-1                 RSQLite_2.2.19              future.apply_1.10.0         intrinsicDimension_1.2.0    data.table_1.14.6           blob_1.2.3                 
[133] S4Vectors_0.36.1            R.oo_1.25.0                 styler_1.7.0                splines_4.2.0               labeling_0.4.2              rematch2_2.1.2             
[139] Cairo_1.6-0                 RCurl_1.98-1.9              hms_1.1.2                   colorspace_2.0-3            GenomicRanges_1.50.2        shape_1.4.6                
[145] nnet_7.3-18                 GEOquery_2.64.2             Rcpp_1.0.9                  RANN_2.6.1                  fansi_1.0.3                 tzdb_0.3.0                 
[151] VIM_6.2.2                   parallelly_1.33.0           R6_2.5.1                    ggridges_0.5.4              lifecycle_1.0.3             zip_2.2.1                  
[157] curl_4.3.3                  leiden_0.4.3                robustbase_0.95-0           Matrix_1.5-1                RcppAnnoy_0.0.20            RColorBrewer_1.1-3         
[163] iterators_1.0.14            spatstat.explore_3.0-5      R.cache_0.16.0              htmlwidgets_1.6.0           polyclip_1.10-4             biomaRt_2.54.0             
[169] purrr_0.3.5                 crosstalk_1.2.0             globals_0.16.2              SCopeLoomR_0.13.0           patchwork_1.1.2             spatstat.random_3.0-1      
[175] slingshot_2.6.0             progressr_0.12.0            codetools_0.2-18            matrixStats_0.63.0          prettyunits_1.1.1           SingleCellExperiment_1.20.0
[181] dbplyr_2.2.1                RSpectra_0.16-1             R.methodsS3_1.8.2           GenomeInfoDb_1.34.4         gtable_0.3.1                DBI_1.1.3                  
[187] stats4_4.2.0                tensor_1.5                  httr_1.4.4                  KernSmooth_2.23-20          stringi_1.7.8               progress_1.2.2             
[193] reshape2_1.4.4              farver_2.1.1                viridis_0.6.2               ggthemes_4.2.4              hexbin_1.28.2               magick_2.7.3               
[199] xml2_1.3.3                  boot_1.3-28                 grr_0.9.5                   readr_2.1.3                 scattermore_1.0             DEoptimR_1.0-11            
[205] bit_4.0.5                   MatrixGenerics_1.10.0       spatstat.data_3.0-0         pkgconfig_2.0.3             TrajectoryUtils_1.6.0
road2you commented 10 months ago

temporary bypass method... https://github.com/thomasp85/ggforce/pull/312#issuecomment-1859660060