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SONGDONGYUAN1994 / PseudotimeDE

A robust DE test method that accounts for the uncertainty in pseudotime inference
MIT License
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Error in PseudotimeDE::runPseudotimeDE(gene.vec = gene.vec, ori.tbl = orig_tbl, : Some cells in sub.tbl are not a subset of ori.tbl #18

Open mcaponegro opened 1 year ago

mcaponegro commented 1 year ago

Hi,

I am interested in implementing your package on my (very large) data. However, I cannot figure out the origin of this error.

I have sampled from the orig_tbl, so the call names must be there. I also checked by running:

 lapply(sub_tbl, function(x) all(x[["cell"]] %in% orig_tbl$cell)) # are all sub in orig?
 [[1]]
 [1] TRUE

 [[2]]
[1] TRUE

 [[3]]
 [1] TRUE

I removed rownames from all data.frames() and even tried subsetting. The error still persists. 

Error in PseudotimeDE::runPseudotimeDE(gene.vec = gene.vec, ori.tbl = orig_tbl,  : 
 Some cells in sub.tbl are not a subset of ori.tbl
Timing stopped at: 0.085 0.004 0.089

Thank you 

sessionInfo()
R version 4.2.0 (2022-04-22)
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/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] 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              
[10] 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] ComplexHeatmap_2.15.4 lubridate_1.9.2       forcats_1.0.0         stringr_1.5.0        
 [5] dplyr_1.1.2           purrr_1.0.1           readr_2.1.4           tidyr_1.3.0          
 [9] tibble_3.2.1          ggplot2_3.4.2         tidyverse_2.0.0       SeuratObject_4.1.3   
[13] Seurat_4.3.0.1       

loaded via a namespace (and not attached):
  [1] utf8_1.2.3                  spatstat.explore_3.2-1      reticulate_1.30            
  [4] tidyselect_1.2.0            htmlwidgets_1.6.2           BiocParallel_1.32.6        
  [7] ranger_0.15.1               gmp_0.7-2                   Rtsne_0.16                 
 [10] munsell_0.5.0               destiny_3.12.0              codetools_0.2-18           
 [13] ica_1.0-3                   future_1.33.0               miniUI_0.1.1.1             
 [16] withr_2.5.0                 spatstat.random_3.1-5       colorspace_2.1-0           
 [19] progressr_0.13.0            Biobase_2.58.0              knitr_1.43                 
 [22] rstudioapi_0.15.0           stats4_4.2.0                SingleCellExperiment_1.20.1
 [25] ROCR_1.0-11                 robustbase_0.99-0           vcd_1.4-11                 
 [28] tensor_1.5                  VIM_6.2.2                   TTR_0.24.3                 
 [31] listenv_0.9.0               labeling_0.4.2              MatrixGenerics_1.10.0      
 [34] GenomeInfoDbData_1.2.9      polyclip_1.10-4             farver_2.1.1               
 [37] pheatmap_1.0.12             PseudotimeDE_1.0.0          parallelly_1.36.0          
 [40] vctrs_0.6.3                 generics_0.1.3              xfun_0.39                  
 [43] timechange_0.2.0            dittoSeq_1.10.0             ggthemes_4.2.4             
 [46] doParallel_1.0.17           R6_2.5.1                    GenomeInfoDb_1.34.9        
 [49] clue_0.3-64                 RcppEigen_0.3.3.9.3         bitops_1.0-7               
 [52] spatstat.utils_3.0-3        DelayedArray_0.24.0         promises_1.2.0.1           
 [55] scales_1.2.1                nnet_7.3-17                 gtable_0.3.3               
 [58] globals_0.16.2              goftest_1.2-3               rlang_1.1.1                
 [61] scatterplot3d_0.3-44        GlobalOptions_0.1.2         splines_4.2.0              
 [64] lazyeval_0.2.2              hexbin_1.28.3               spatstat.geom_3.2-2        
 [67] BiocManager_1.30.21         yaml_2.3.7                  reshape2_1.4.4             
 [70] abind_1.4-5                 httpuv_1.6.11               tools_4.2.0                
 [73] ellipsis_0.3.2              RColorBrewer_1.1-3          proxy_0.4-27               
 [76] BiocGenerics_0.44.0         ggridges_0.5.4              Rcpp_1.0.11                
 [79] plyr_1.8.8                  zlibbioc_1.44.0             RCurl_1.98-1.12            
 [82] deldir_1.0-9                GetoptLong_1.0.5            pbapply_1.7-2              
 [85] viridis_0.6.3               cowplot_1.1.1               S4Vectors_0.36.2           
 [88] zoo_1.8-12                  SummarizedExperiment_1.28.0 ggrepel_0.9.3              
 [91] cluster_2.1.3               magrittr_2.0.3              data.table_1.14.8          
 [94] RSpectra_0.16-1             scattermore_1.2             circlize_0.4.15            
 [97] lmtest_0.9-40               RANN_2.6.1                  pcaMethods_1.90.0          
[100] fitdistrplus_1.1-11         matrixStats_1.0.0           hms_1.1.3                  
[103] patchwork_1.1.2             mime_0.12                   evaluate_0.21              
[106] xtable_1.8-4                smoother_1.1                shape_1.4.6                
[109] IRanges_2.32.0              gridExtra_2.3               compiler_4.2.0             
[112] crayon_1.5.2                KernSmooth_2.23-20          htmltools_0.5.5            
[115] tzdb_0.4.0                  later_1.3.1                 ClusterR_1.3.1             
[118] MASS_7.3-56                 boot_1.3-28                 Matrix_1.6-0               
[121] car_3.1-2                   cli_3.6.1                   parallel_4.2.0             
[124] igraph_1.5.0                GenomicRanges_1.50.2        pkgconfig_2.0.3            
[127] laeken_0.5.2                sp_2.0-0                    plotly_4.10.2              
[130] spatstat.sparse_3.0-2       foreach_1.5.2               paletteer_1.5.0            
[133] XVector_0.38.0              digest_0.6.33               sctransform_0.3.5          
[136] RcppAnnoy_0.0.21            spatstat.data_3.0-1         rmarkdown_2.23             
[139] leiden_0.4.3                uwot_0.1.16                 curl_5.0.1                 
[142] shiny_1.7.4.1               ggplot.multistats_1.0.0     rjson_0.2.21               
[145] lifecycle_1.0.3             nlme_3.1-157                jsonlite_1.8.7             
[148] carData_3.0-5               viridisLite_0.4.2           fansi_1.0.4                
[151] pillar_1.9.0                lattice_0.20-45             fastmap_1.1.1              
[154] httr_1.4.6                  DEoptimR_1.1-0              survival_3.3-1             
[157] glue_1.6.2                  xts_0.13.1                  remotes_2.4.2              
[160] iterators_1.0.14            png_0.1-8                   class_7.3-20               
[163] presto_1.0.0                stringi_1.7.12              rematch2_2.1.2             
[166] RcppHNSW_0.4.1              renv_1.0.0                  knn.covertree_1.0          
[169] irlba_2.3.5.1               e1071_1.7-13                future.apply_1.11.0
SONGDONGYUAN1994 commented 1 year ago

@mcaponegro Hi, Sorry that without demo data I cannot reproduce your error. I updated the package and could you please re-install it? Now it will tell you which sub is problematic. Please let me know how it works now and thanks!

Best, Dongyuan

mcaponegro commented 1 year ago

Hi, thankyou for the reply. No luck with the install. Here is a dput version of a subset of my data for reproducibility:

orig_tbl_test <- structure(list(cell = c("Cx05_S0_c_1_45_670", "Cx05_S1_c_2_275_278", 
"Cx05_S1_c_2_37_110", "Cx06_S1_c_2_32_999", "Cx05_S2_c_3_60_47", 
"Cx06_S0_c_1_105_149", "Cx05_S3_c_4_164_130", "Cx05_S3_c_4_122_708", 
"Cx06_S0_c_1_100_696", "Cx06_S0_c_1_93_1224", "Cx06_S0_c_1_46_818", 
"Cx05_S1_c_2_64_108", "Cx06_S3_c_4_6_766", "Cx05_S3_c_4_211_508", 
"Cx05_S2_c_3_94_363", "Cx05_S3_c_4_299_356", "Cx05_S2_c_3_71_204", 
"Cx05_S1_c_2_159_1106", "Cx06_S0_c_1_36_692", "Cx05_S3_c_4_105_278", 
"Cx05_S3_c_4_156_250", "Cx06_S0_c_1_126_1608", "Cx06_S0_c_1_26_677", 
"Cx05_S2_c_3_42_687", "Cx05_S3_c_4_66_247", "Cx06_S2_c_3_33_1272", 
"Cx06_S0_c_1_108_536", "Cx05_S3_c_4_42_41", "Cx06_S0_c_1_129_2098", 
"Cx05_S1_c_2_67_139", "Cx05_S3_c_4_32_1159", "Cx06_S0_c_1_16_2056", 
"Cx06_S2_c_3_101_287", "Cx05_S1_c_2_235_478", "Cx05_S2_c_3_87_1032", 
"Cx06_S0_c_1_76_303", "Cx06_S0_c_1_122_842", "Cx05_S0_c_1_25_152", 
"Cx05_S2_c_3_12_1213", "Cx06_S1_c_2_91_536", "Cx05_S1_c_2_150_40", 
"Cx06_S1_c_2_73_764", "Cx05_S3_c_4_185_832", "Cx05_S3_c_4_269_357", 
"Cx05_S1_c_2_174_443", "Cx06_S0_c_1_104_930", "Cx06_S2_c_3_90_380", 
"Cx05_S3_c_4_196_274", "Cx05_S3_c_4_27_238", "Cx05_S2_c_3_72_384", 
"Cx06_S2_c_3_140_782", "Cx06_S2_c_3_147_368", "Cx06_S3_c_4_90_235", 
"Cx05_S2_c_3_2_115", "Cx06_S2_c_3_80_776", "Cx05_S2_c_3_95_476", 
"Cx06_S3_c_4_22_1761", "Cx06_S2_c_3_54_210", "Cx05_S3_c_4_45_225", 
"Cx05_S1_c_2_279_1386", "Cx05_S1_c_2_71_155", "Cx05_S3_c_4_42_77", 
"Cx05_S1_c_2_88_932", "Cx06_S2_c_3_37_749", "Cx05_S2_c_3_39_698", 
"Cx06_S2_c_3_26_720", "Cx05_S1_c_2_281_258", "Cx05_S3_c_4_118_74", 
"Cx05_S3_c_4_123_173", "Cx05_S0_c_1_70_264", "Cx06_S1_c_2_71_409", 
"Cx05_S3_c_4_265_307", "Cx05_S1_c_2_136_137", "Cx05_S3_c_4_255_331", 
"Cx05_S1_c_2_113_140", "Cx06_S2_c_3_101_606", "Cx06_S0_c_1_76_399", 
"Cx05_S3_c_4_24_132", "Cx05_S2_c_3_14_227", "Cx06_S0_c_1_11_1244", 
"Cx05_S1_c_2_146_1461", "Cx05_S1_c_2_114_656", "Cx05_S2_c_3_7_284", 
"Cx06_S2_c_3_26_585", "Cx05_S2_c_3_47_336", "Cx05_S3_c_4_145_317", 
"Cx06_S2_c_3_124_813", "Cx06_S3_c_4_22_319", "Cx06_S3_c_4_86_1570", 
"Cx06_S3_c_4_24_1137", "Cx05_S0_c_1_81_385", "Cx06_S0_c_1_118_112", 
"Cx06_S2_c_3_61_1609", "Cx05_S1_c_2_76_469", "Cx06_S0_c_1_110_76", 
"Cx05_S1_c_2_284_697", "Cx06_S2_c_3_49_565", "Cx05_S2_c_3_20_324", 
"Cx05_S2_c_3_71_122", "Cx06_S3_c_4_85_1126", "Cx05_S1_c_2_183_396", 
"Cx05_S2_c_3_89_133", "Cx06_S0_c_1_10_2479", "Cx05_S3_c_4_45_591", 
"Cx05_S3_c_4_128_761", "Cx05_S3_c_4_61_919", "Cx05_S1_c_2_221_209", 
"Cx05_S0_c_1_8_749", "Cx06_S2_c_3_147_175", "Cx05_S3_c_4_104_11", 
"Cx05_S3_c_4_84_104", "Cx06_S0_c_1_27_338", "Cx05_S1_c_2_185_506", 
"Cx06_S2_c_3_113_745", "Cx05_S0_c_1_78_384", "Cx06_S1_c_2_25_1217", 
"Cx06_S0_c_1_29_442", "Cx06_S0_c_1_28_789", "Cx06_S2_c_3_71_1078", 
"Cx05_S1_c_2_192_553", "Cx06_S3_c_4_79_564", "Cx05_S0_c_1_84_200", 
"Cx05_S3_c_4_192_1171", "Cx05_S0_c_1_43_209", "Cx05_S3_c_4_181_68", 
"Cx05_S1_c_2_131_36", "Cx06_S0_c_1_9_1272", "Cx05_S0_c_1_46_806", 
"Cx05_S1_c_2_98_954", "Cx05_S3_c_4_269_523", "Cx05_S1_c_2_89_524", 
"Cx06_S1_c_2_26_201", "Cx05_S3_c_4_217_211", "Cx06_S0_c_1_63_559", 
"Cx06_S0_c_1_6_3174", "Cx06_S0_c_1_80_678", "Cx05_S1_c_2_266_440", 
"Cx05_S0_c_1_66_201", "Cx06_S0_c_1_5_1199", "Cx06_S1_c_2_65_737", 
"Cx05_S1_c_2_264_589", "Cx06_S2_c_3_12_1892", "Cx06_S0_c_1_66_34", 
"Cx05_S3_c_4_52_774", "Cx05_S1_c_2_95_489", "Cx06_S2_c_3_126_429", 
"Cx05_S1_c_2_219_209", "Cx05_S1_c_2_81_838", "Cx06_S0_c_1_9_765", 
"Cx06_S1_c_2_38_1121", "Cx06_S2_c_3_4_375", "Cx05_S3_c_4_114_84", 
"Cx06_S2_c_3_71_102", "Cx05_S3_c_4_95_99", "Cx06_S2_c_3_54_889", 
"Cx05_S3_c_4_85_559", "Cx05_S1_c_2_108_353", "Cx05_S0_c_1_9_435", 
"Cx05_S1_c_2_186_120", "Cx05_S1_c_2_206_154", "Cx05_S1_c_2_81_198", 
"Cx06_S2_c_3_68_653", "Cx05_S2_c_3_33_162", "Cx06_S2_c_3_75_1174", 
"Cx05_S2_c_3_77_112", "Cx06_S3_c_4_2_290", "Cx06_S2_c_3_114_627", 
"Cx06_S0_c_1_18_3344", "Cx06_S0_c_1_121_2259", "Cx05_S1_c_2_143_829", 
"Cx05_S3_c_4_292_213", "Cx06_S0_c_1_93_692", "Cx06_S2_c_3_3_1445", 
"Cx05_S1_c_2_97_52", "Cx06_S2_c_3_142_730", "Cx06_S0_c_1_1_594", 
"Cx06_S0_c_1_17_1115", "Cx06_S2_c_3_63_722", "Cx05_S1_c_2_201_478", 
"Cx05_S2_c_3_66_691", "Cx05_S3_c_4_196_122", "Cx05_S0_c_1_17_289", 
"Cx05_S3_c_4_282_532", "Cx05_S0_c_1_73_167", "Cx05_S2_c_3_38_556", 
"Cx06_S0_c_1_16_208", "Cx05_S3_c_4_138_532", "Cx05_S0_c_1_15_9", 
"Cx05_S2_c_3_17_630", "Cx05_S1_c_2_110_269", "Cx05_S3_c_4_262_554", 
"Cx06_S0_c_1_2_534", "Cx05_S1_c_2_155_684", "Cx06_S2_c_3_52_736", 
"Cx06_S3_c_4_3_673", "Cx06_S2_c_3_25_2179", "Cx05_S3_c_4_13_768", 
"Cx05_S2_c_3_56_648", "Cx06_S1_c_2_47_926", "Cx05_S1_c_2_204_635"
), pseudotime = c(1, 118, 37, 30, 21, 67, 111, 149, 75, 131, 
2, 23, 80, 80, 18, 123, 35, 104, 1, 143, 145, 78, 41, 70, 112, 
46, 90, 147, 84, 27, 142, 51, 26, 33, 40, 95, 84, 11, 101, 54, 
145, 32, 95, 116, 38, 97, 39, 97, 85, 45, 40, 90, 68, 63, 46, 
22, 54, 47, 131, 145, 70, 142, 107, 47, 87, 57, 128, 145, 137, 
50, 80, 106, 128, 132, 132, 24, 84, 115, 25, 66, 145, 128, 63, 
45, 14, 137, 21, 65, 90, 22, 25, 6, 60, 72, 19, 118, 43, 39, 
35, 87, 38, 28, 52, 143, 150, 150, 28, 9, 87, 149, 147, 76, 33, 
78, 19, 32, 44, 6, 55, 77, 64, 56, 97, 50, 115, 95, 69, 2, 116, 
120, 130, 12, 64, 17, 77, 101, 93, 54, 65, 15, 134, 66, 4, 138, 
131, 16, 133, 117, 87, 37, 61, 132, 41, 138, 59, 107, 126, 11, 
25, 22, 119, 68, 5, 48, 6, 75, 39, 75, 74, 95, 91, 146, 90, 118, 
48, 76, 46, 62, 33, 42, 93, 47, 139, 37, 5, 79, 134, 10, 41, 
119, 143, 79, 93, 67, 54, 49, 117, 28, 29, 34)), row.names = c("Cx05_S0_c_1_45_670", 
"Cx05_S1_c_2_275_278", "Cx05_S1_c_2_37_110", "Cx06_S1_c_2_32_999", 
"Cx05_S2_c_3_60_47", "Cx06_S0_c_1_105_149", "Cx05_S3_c_4_164_130", 
"Cx05_S3_c_4_122_708", "Cx06_S0_c_1_100_696", "Cx06_S0_c_1_93_1224", 
"Cx06_S0_c_1_46_818", "Cx05_S1_c_2_64_108", "Cx06_S3_c_4_6_766", 
"Cx05_S3_c_4_211_508", "Cx05_S2_c_3_94_363", "Cx05_S3_c_4_299_356", 
"Cx05_S2_c_3_71_204", "Cx05_S1_c_2_159_1106", "Cx06_S0_c_1_36_692", 
"Cx05_S3_c_4_105_278", "Cx05_S3_c_4_156_250", "Cx06_S0_c_1_126_1608", 
"Cx06_S0_c_1_26_677", "Cx05_S2_c_3_42_687", "Cx05_S3_c_4_66_247", 
"Cx06_S2_c_3_33_1272", "Cx06_S0_c_1_108_536", "Cx05_S3_c_4_42_41", 
"Cx06_S0_c_1_129_2098", "Cx05_S1_c_2_67_139", "Cx05_S3_c_4_32_1159", 
"Cx06_S0_c_1_16_2056", "Cx06_S2_c_3_101_287", "Cx05_S1_c_2_235_478", 
"Cx05_S2_c_3_87_1032", "Cx06_S0_c_1_76_303", "Cx06_S0_c_1_122_842", 
"Cx05_S0_c_1_25_152", "Cx05_S2_c_3_12_1213", "Cx06_S1_c_2_91_536", 
"Cx05_S1_c_2_150_40", "Cx06_S1_c_2_73_764", "Cx05_S3_c_4_185_832", 
"Cx05_S3_c_4_269_357", "Cx05_S1_c_2_174_443", "Cx06_S0_c_1_104_930", 
"Cx06_S2_c_3_90_380", "Cx05_S3_c_4_196_274", "Cx05_S3_c_4_27_238", 
"Cx05_S2_c_3_72_384", "Cx06_S2_c_3_140_782", "Cx06_S2_c_3_147_368", 
"Cx06_S3_c_4_90_235", "Cx05_S2_c_3_2_115", "Cx06_S2_c_3_80_776", 
"Cx05_S2_c_3_95_476", "Cx06_S3_c_4_22_1761", "Cx06_S2_c_3_54_210", 
"Cx05_S3_c_4_45_225", "Cx05_S1_c_2_279_1386", "Cx05_S1_c_2_71_155", 
"Cx05_S3_c_4_42_77", "Cx05_S1_c_2_88_932", "Cx06_S2_c_3_37_749", 
"Cx05_S2_c_3_39_698", "Cx06_S2_c_3_26_720", "Cx05_S1_c_2_281_258", 
"Cx05_S3_c_4_118_74", "Cx05_S3_c_4_123_173", "Cx05_S0_c_1_70_264", 
"Cx06_S1_c_2_71_409", "Cx05_S3_c_4_265_307", "Cx05_S1_c_2_136_137", 
"Cx05_S3_c_4_255_331", "Cx05_S1_c_2_113_140", "Cx06_S2_c_3_101_606", 
"Cx06_S0_c_1_76_399", "Cx05_S3_c_4_24_132", "Cx05_S2_c_3_14_227", 
"Cx06_S0_c_1_11_1244", "Cx05_S1_c_2_146_1461", "Cx05_S1_c_2_114_656", 
"Cx05_S2_c_3_7_284", "Cx06_S2_c_3_26_585", "Cx05_S2_c_3_47_336", 
"Cx05_S3_c_4_145_317", "Cx06_S2_c_3_124_813", "Cx06_S3_c_4_22_319", 
"Cx06_S3_c_4_86_1570", "Cx06_S3_c_4_24_1137", "Cx05_S0_c_1_81_385", 
"Cx06_S0_c_1_118_112", "Cx06_S2_c_3_61_1609", "Cx05_S1_c_2_76_469", 
"Cx06_S0_c_1_110_76", "Cx05_S1_c_2_284_697", "Cx06_S2_c_3_49_565", 
"Cx05_S2_c_3_20_324", "Cx05_S2_c_3_71_122", "Cx06_S3_c_4_85_1126", 
"Cx05_S1_c_2_183_396", "Cx05_S2_c_3_89_133", "Cx06_S0_c_1_10_2479", 
"Cx05_S3_c_4_45_591", "Cx05_S3_c_4_128_761", "Cx05_S3_c_4_61_919", 
"Cx05_S1_c_2_221_209", "Cx05_S0_c_1_8_749", "Cx06_S2_c_3_147_175", 
"Cx05_S3_c_4_104_11", "Cx05_S3_c_4_84_104", "Cx06_S0_c_1_27_338", 
"Cx05_S1_c_2_185_506", "Cx06_S2_c_3_113_745", "Cx05_S0_c_1_78_384", 
"Cx06_S1_c_2_25_1217", "Cx06_S0_c_1_29_442", "Cx06_S0_c_1_28_789", 
"Cx06_S2_c_3_71_1078", "Cx05_S1_c_2_192_553", "Cx06_S3_c_4_79_564", 
"Cx05_S0_c_1_84_200", "Cx05_S3_c_4_192_1171", "Cx05_S0_c_1_43_209", 
"Cx05_S3_c_4_181_68", "Cx05_S1_c_2_131_36", "Cx06_S0_c_1_9_1272", 
"Cx05_S0_c_1_46_806", "Cx05_S1_c_2_98_954", "Cx05_S3_c_4_269_523", 
"Cx05_S1_c_2_89_524", "Cx06_S1_c_2_26_201", "Cx05_S3_c_4_217_211", 
"Cx06_S0_c_1_63_559", "Cx06_S0_c_1_6_3174", "Cx06_S0_c_1_80_678", 
"Cx05_S1_c_2_266_440", "Cx05_S0_c_1_66_201", "Cx06_S0_c_1_5_1199", 
"Cx06_S1_c_2_65_737", "Cx05_S1_c_2_264_589", "Cx06_S2_c_3_12_1892", 
"Cx06_S0_c_1_66_34", "Cx05_S3_c_4_52_774", "Cx05_S1_c_2_95_489", 
"Cx06_S2_c_3_126_429", "Cx05_S1_c_2_219_209", "Cx05_S1_c_2_81_838", 
"Cx06_S0_c_1_9_765", "Cx06_S1_c_2_38_1121", "Cx06_S2_c_3_4_375", 
"Cx05_S3_c_4_114_84", "Cx06_S2_c_3_71_102", "Cx05_S3_c_4_95_99", 
"Cx06_S2_c_3_54_889", "Cx05_S3_c_4_85_559", "Cx05_S1_c_2_108_353", 
"Cx05_S0_c_1_9_435", "Cx05_S1_c_2_186_120", "Cx05_S1_c_2_206_154", 
"Cx05_S1_c_2_81_198", "Cx06_S2_c_3_68_653", "Cx05_S2_c_3_33_162", 
"Cx06_S2_c_3_75_1174", "Cx05_S2_c_3_77_112", "Cx06_S3_c_4_2_290", 
"Cx06_S2_c_3_114_627", "Cx06_S0_c_1_18_3344", "Cx06_S0_c_1_121_2259", 
"Cx05_S1_c_2_143_829", "Cx05_S3_c_4_292_213", "Cx06_S0_c_1_93_692", 
"Cx06_S2_c_3_3_1445", "Cx05_S1_c_2_97_52", "Cx06_S2_c_3_142_730", 
"Cx06_S0_c_1_1_594", "Cx06_S0_c_1_17_1115", "Cx06_S2_c_3_63_722", 
"Cx05_S1_c_2_201_478", "Cx05_S2_c_3_66_691", "Cx05_S3_c_4_196_122", 
"Cx05_S0_c_1_17_289", "Cx05_S3_c_4_282_532", "Cx05_S0_c_1_73_167", 
"Cx05_S2_c_3_38_556", "Cx06_S0_c_1_16_208", "Cx05_S3_c_4_138_532", 
"Cx05_S0_c_1_15_9", "Cx05_S2_c_3_17_630", "Cx05_S1_c_2_110_269", 
"Cx05_S3_c_4_262_554", "Cx06_S0_c_1_2_534", "Cx05_S1_c_2_155_684", 
"Cx06_S2_c_3_52_736", "Cx06_S3_c_4_3_673", "Cx06_S2_c_3_25_2179", 
"Cx05_S3_c_4_13_768", "Cx05_S2_c_3_56_648", "Cx06_S1_c_2_47_926", 
"Cx05_S1_c_2_204_635"), class = "data.frame")

sub_tbl_test <- list(structure(list(cell = c("Cx05_S1_c_2_143_829", "Cx05_S1_c_2_185_506", 
"Cx05_S1_c_2_275_278", "Cx05_S2_c_3_17_630", "Cx05_S2_c_3_20_324", 
"Cx05_S3_c_4_123_173", "Cx05_S3_c_4_156_250", "Cx05_S3_c_4_52_774", 
"Cx06_S0_c_1_100_696", "Cx06_S0_c_1_118_112", "Cx06_S0_c_1_17_1115", 
"Cx06_S2_c_3_147_175", "Cx06_S2_c_3_147_368", "Cx06_S2_c_3_68_653", 
"Cx06_S3_c_4_3_673"), pseudotime = c(115, 71, 39, 128, 97, 44, 
60, 19, 66, 4, 21, 98, 32, 133, 101)), row.names = c(1433L, 2091L, 
3223L, 4481L, 4519L, 6018L, 6524L, 9142L, 9911L, 10287L, 10721L, 
13738L, 13740L, 15161L, 15864L), class = "data.frame"), structure(list(
    cell = c("Cx05_S0_c_1_66_201", "Cx05_S1_c_2_150_40", "Cx05_S2_c_3_12_1213", 
    "Cx05_S2_c_3_87_1032", "Cx06_S0_c_1_105_149", "Cx06_S0_c_1_118_112", 
    "Cx06_S0_c_1_36_692", "Cx06_S0_c_1_80_678", "Cx06_S2_c_3_101_287", 
    "Cx06_S3_c_4_24_1137", "Cx06_S3_c_4_79_564", "Cx06_S3_c_4_86_1570"
    ), pseudotime = c(23, 116, 63, 65, 75, 137, 31, 94, 95, 100, 
    122, 22)), row.names = c(466L, 1622L, 4259L, 5540L, 10056L, 
10304L, 11124L, 11825L, 13349L, 15823L, 16213L, 16279L), class = "data.frame"), 
    structure(list(cell = c("Cx05_S0_c_1_78_384", "Cx05_S2_c_3_66_691", 
    "Cx05_S3_c_4_123_173", "Cx05_S3_c_4_145_317", "Cx05_S3_c_4_156_250", 
    "Cx05_S3_c_4_185_832", "Cx05_S3_c_4_32_1159", "Cx06_S0_c_1_122_842", 
    "Cx06_S0_c_1_16_2056", "Cx06_S2_c_3_25_2179", "Cx06_S2_c_3_37_749", 
    "Cx06_S2_c_3_80_776", "Cx06_S3_c_4_2_290"), pseudotime = c(111, 
    147, 111, 31, 148, 106, 10, 40, 24, 57, 53, 44, 89)), row.names = c(574L, 
    5359L, 5996L, 6355L, 6529L, 7126L, 8784L, 10575L, 10841L, 
    14195L, 14594L, 15503L, 15726L), class = "data.frame"))

gene.vec <- c("AATK", "ABL1", "ABL2", "ACACB", "ACE", "ACKR1", "ACKR3", "ACKR4", 
"ACTA2", "ACTG2", "ACVR1", "ACVR1B", "ACVR2A", "ACVRL1", "ADGRA2", 
"ADGRA3", "ADGRE2", "ADGRE5", "ADGRF1", "ADGRF3", "ADGRF5", "ADGRG1", 
"ADGRG3", "ADGRG5", "ADGRG6", "ADGRL1", "ADGRL2", "ADGRL4", "ADGRV1", 
"ADIPOQ", "ADIRF", "ADM2", "AGR2", "AHI1", "AHR", "AIF1", "AKT1", 
"ALCAM", "ANGPT1", "ANGPT2", "ANGPTL1", "ANKRD1", "ANXA1", "ANXA2", 
"ANXA4", "APOA1", "APOC1", "APOD", "APOE", "APP", "AQP3", "AR", 
"AREG", "ARF1", "ARG1", "ARHGDIB", "ARID5B", "ATF3", "ATG10", 
"ATG12", "ATG5", "ATM", "ATP5F1E", "ATR", "AXL", "AZGP1", "AZU1", 
"B2M", "B3GNT7", "BAG3", "BATF", "BAX", "BBLN", "BCL2", "BCL2L1", 
"BCL6", "BDCA2", "BECN1", "BEST1", "BEST4", "BGN", "BID", "BIRC5", 
"BMP1", "BMP2", "BMP3", "BMP4", "BMP5", "BMP7", "BMPR1A", "BMPR2", 
"BRCA1", "BST1", "BST2", "BTF3", "BTG1", "BTK", "C11orf96", "C1QA", 
"C1QB", "C1QC", "C5AR2", "CACNA1C", "CALB1", "CALD1", "CALM1", 
"CALM2", "CALM3", "CAMP", "CARMN", "CASP3", "CASP8", "CASR", 
"CAV1", "CCL11", "CCL13", "CCL15", "CCL17", "CCL18", "CCL19", 
"CCL2", "CCL20", "CCL21", "CCL22", "CCL26", "CCL27", "CCL28", 
"CCL3/L1/L3", "CCL4/L1/L2", "CCL5", "CCL8", "CCND1", "CCR1", 
"CCR10", "CCR2", "CCR4", "CCR5", "CCR6", "CCR7", "CCRL2", "CD14", 
"CD163", "CD164", "CD19", "CD1C", "CD2", "CD207", "CD209", "CD24", 
"CD27", "CD274", "CD276", "CD28", "CD300A", "CD33", "CD34", "CD36", 
"CD37", "CD38", "CD3D", "CD3E", "CD3G", "CD4", "CD40", "CD40LG", 
"CD44", "CD47", "CD48", "CD52", "CD53", "CD55", "CD58", "CD59", 
"CD5L", "CD63", "CD68", "CD69", "CD70", "CD74", "CD79A", "CD80", 
"CD81", "CD83", "CD84", "CD86", "CD8A", "CD8B", "CD9", "CDH1", 
"CDH11", "CDH19", "CDH5", "CDKN1A", "CDKN3", "CEACAM1", "CEACAM6", 
"CELSR1", "CELSR2", "CENPF", "CFD", "CFLAR", "CHEK1", "CHEK2", 
"CHI3L1", "CIDEA", "CIITA", "CLCF1", "CLDN1", "CLDN4", "CLEC10A", 
"CLEC12A", "CLEC14A", "CLEC1A", "CLEC2B", "CLEC2D", "CLEC4A", 
"CLEC4D", "CLEC4E", "CLEC5A", "CLEC7A", "CLOCK", "CLU", "CMKLR1", 
"CNTFR", "COL11A1", "COL12A1", "COL14A1", "COL15A1", "COL16A1", 
"COL17A1", "COL18A1", "COL1A1", "COL1A2", "COL21A1", "COL27A1", 
"COL3A1", "COL4A1", "COL4A2", "COL4A5", "COL5A1", "COL5A2", "COL5A3", 
"COL6A1", "COL6A2", "COL6A3", "COL8A1", "COL9A2", "COL9A3", "COTL1", 
"CPA3", "CPB1", "CRIP1", "CRP", "CRYAB", "CSF1", "CSF1R", "CSF2", 
"CSF2RA", "CSF2RB", "CSF3", "CSF3R", "CSHL1", "CSK", "CST7", 
"CTLA4", "CTNNB1", "CTSG", "CTSH", "CTSW", "CUZD1", "CX3CL1", 
"CX3CR1", "CXCL1/2/3", "CXCL10", "CXCL12", "CXCL13", "CXCL14", 
"CXCL16", "CXCL17", "CXCL5", "CXCL8", "CXCL9", "CXCR1", "CXCR2", 
"CXCR3", "CXCR4", "CXCR5", "CXCR6", "CYP1B1", "CYP2U1", "CYSTM1", 
"CYTOR", "DCN", "DDC", "DDIT3", "DDR1", "DDR2", "DDX58", "DHRS2", 
"DLL1", "DLL4", "DMBT1", "DNMT1", "DNMT3A", "DPP4", "DST", "DUSP1", 
"DUSP2", "DUSP4", "DUSP5", "DUSP6", "EBI3", "EFNA1", "EFNA4", 
"EFNA5", "EFNB1", "EFNB2", "EGF", "EGFR", "EIF5A/L1", "ELANE", 
"EMP3", "ENG", "ENO1", "ENTPD1", "EOMES", "EPCAM", "EPHA2", "EPHA3", 
"EPHA4", "EPHA7", "EPHB2", "EPHB3", "EPHB4", "EPHB6", "EPOR", 
"ERBB2", "ERBB3", "EREG", "ESAM", "ESR1", "ETS1", "ETV4", "ETV5", 
"EZH2", "EZR", "FABP4", "FABP5", "FAM30A", "FAP", "FAS", "FASLG", 
"FASN", "FAU", "FCER1A", "FCER1G", "FCGBP", "FCGR3A/B", "FCRL3", 
"FCRL5", "FCRLA", "FES", "FFAR2", "FFAR3", "FFAR4", "FGF1", "FGF12", 
"FGF13", "FGF18", "FGF2", "FGF7", "FGF9", "FGFR1", "FGFR2", "FGFR3", 
"FGG", "FGR", "FHIT", "FKBP11", "FKBP5", "FLT1", "FLT3LG", "FN1", 
"FOS", "FOXF1", "FOXP3", "FPR1", "FYB1", "FYN", "FZD1", "FZD3", 
"FZD4", "FZD5", "FZD6", "FZD7", "FZD8", "G6PD", "GADD45B", "GAS6", 
"GATA3", "GC", "GCG", "GDF15", "GLUD1", "GLUL", "GNLY", "GPBAR1", 
"GPER1", "GPNMB", "GPR183", "GPX1", "GPX3", "GSN", "GSTP1", "GZMA", 
"GZMB", "GZMH", "GZMK", "H2AZ1", "H4C3", "HAVCR2", "HBA1/2", 
"HBB", "HCAR2/3", "HCK", "HCST", "HDAC1", "HDAC11", "HDAC3", 
"HDAC4", "HDAC5", "HEY1", "HGF", "HIF1A", "HILPDA", "HLA-DPA1", 
"HLA-DPB1", "HLA-DQA1", "HLA-DQB1/2", "HLA-DRA", "HLA-DRB", "HMGB2", 
"HMGN2", "HPGDS", "HSD17B2", "HSP90AA1", "HSP90AB1", "HSP90B1", 
"HSPA1A/B", "HSPB1", "HTT", "IAPP", "ICA1", "ICAM1", "ICAM2", 
"ICAM3", "ICOS", "ICOSLG", "IDO1", "IER3", "IFI27", "IFI44L", 
"IFIH1", "IFIT1", "IFIT3", "IFITM1", "IFITM3", "IFNA1/13", "IFNAR1", 
"IFNAR2", "IFNG", "IFNGR1", "IFNGR2", "IFNL2/3", "IGF1", "IGF1R", 
"IGF2", "IGF2R", "IGFBP3", "IGFBP5", "IGFBP6", "IGFBP7", "IGHA1", 
"IGHD", "IGHG1", "IGHG2", "IGHM", "IGKC", "IKZF3", "IL10", "IL10RA", 
"IL10RB", "IL11", "IL11RA", "IL12A", "IL12B", "IL12RB1", "IL12RB2", 
"IL13", "IL13RA1", "IL15", "IL15RA", "IL16", "IL17A", "IL17B", 
"IL17D", "IL17F", "IL17RA", "IL17RB", "IL17RE", "IL18", "IL18R1", 
"IL1A", "IL1B", "IL1R1", "IL1R2", "IL1RAP", "IL1RL1", "IL1RN", 
"IL2", "IL20", "IL20RA", "IL21", "IL21R", "IL22", "IL22RA1", 
"IL23A", "IL23R", "IL24", "IL25", "IL27RA", "IL2RA", "IL2RB", 
"IL2RG", "IL32", "IL33", "IL34", "IL36G", "IL3RA", "IL4R", "IL5RA", 
"IL6", "IL6R", "IL6ST", "IL7", "IL7R", "ILT7", "INHA", "INHBA", 
"INHBB", "INS", "INSR", "IRF3", "IRF4", "ITGA1", "ITGA2", "ITGA3", 
"ITGA5", "ITGA6", "ITGA8", "ITGA9", "ITGAE", "ITGAL", "ITGAM", 
"ITGAV", "ITGAX", "ITGB1", "ITGB2", "ITGB4", "ITGB5", "ITGB6", 
"ITGB8", "ITK", "ITM2A", "JAG1", "JAK1", "JAK2", "JCHAIN", "JUN", 
"JUNB", "KDR", "KIT", "KITLG", "KLF2", "KLK3", "KLRB1", "KLRF1", 
"KLRK1", "KRAS", "KRT1", "KRT10", "KRT13", "KRT14", "KRT15", 
"KRT16", "KRT17", "KRT18", "KRT19", "KRT20", "KRT23", "KRT4", 
"KRT5", "KRT6A/B/C", "KRT7", "KRT8", "KRT80", "KRT86", "LAG3", 
"LAIR1", "LAMP2", "LAMP3", "LCN2", "LDB2", "LDHA", "LDLR", "LEFTY1", 
"LEP", "LGALS1", "LGALS3", "LGALS3BP", "LGALS9", "LGR5", "LIF", 
"LIFR", "LILRB4", "LINC01781", "LINC01857", "LINC02446", "LMNA", 
"LPAR5", "LRRC15", "LTB", "LTBR", "LTF", "LUM", "LY6D", "LY75", 
"LYN", "LYZ", "MAF", "MALAT1", "MAML2", "MAP1LC3B/2", "MAPK13", 
"MAPK14", "MARCO", "MB", "MECOM", "MEG3", "MERTK", "MET", "MFAP5", 
"MGP", "MHC I", "MIF", "MIR4435-2HG", "MKI67", "MMP1", "MMP12", 
"MMP14", "MMP19", "MMP2", "MMP7", "MMP9", "MPO", "MRC1", "MRC2", 
"MS4A1", "MS4A2", "MS4A4A", "MS4A6A", "MSC", "MSMB", "MSR1", 
"MST1R", "MT1X", "MT2A", "MTOR", "MUC2", "MX1", "MXRA8", "MYC", 
"MYH11", "MYH6", "MYL12A", "MYL4", "MYL7", "MYL9", "MZB1", "MZT2A/B", 
"NACA", "NANOG", "NCR1", "NDRG1", "NEAT1", "NELL2", "NFKB1", 
"NFKBIA", "NGFR", "NKG7", "NLRC4", "NLRC5", "NLRP1", "NLRP2", 
"NLRP3", "NOD2", "NOSIP", "NOTCH1", "NOTCH2", "NOTCH3", "NPPC", 
"NPR1", "NPR2", "NPR3", "NR1H2", "NR1H3", "NR3C1", "NR4A1", "NRG1", 
"NRXN1", "NRXN3", "NTRK2", "NUSAP1", "NegativeAdd", "OAS1", "OAS2", 
"OAS3", "OASL", "OLFM4", "OLR1", "OSM", "OSMR", "P2RX5", "PARP1", 
"PCNA", "PDCD1", "PDCD1LG2", "PDGFA", "PDGFB", "PDGFC", "PDGFD", 
"PDGFRA", "PDGFRB", "PDPN", "PDS5A", "PECAM1", "PF4/V1", "PFN1", 
"PGF", "PGR", "PHLDA2", "PIGR", "PIK3IP1", "PLAC8", "PLAC9", 
"PMEL", "PNOC", "POU5F1", "PPARA", "PPARD", "PPARG", "PPIA", 
"PRF1", "PRSS2", "PRTN3", "PSAP", "PSCA", "PSD3", "PTGDR2", "PTGDS", 
"PTGES", "PTGES2", "PTGES3", "PTGIS", "PTGS1", "PTGS2", "PTK2", 
"PTK6", "PTPRC", "PTPRCAP", "PTTG1", "Pan-Microbial-16S", "QRFPR", 
"RAC1", "RAC2", "RACK1", "RAG1", "RAMP1", "RAMP2", "RAMP3", "RARA", 
"RARB", "RARG", "RARRES1", "RARRES2", "RB1", "RBM47", "RBPJ", 
"REG1A", "RELA", "RELT", "RGCC", "RGS1", "RGS2", "RGS5", "RNF43", 
"ROR1", "RORA", "RORC", "RPL21", "RPL22", "RPL32", "RPL34", "RPL37", 
"RPS4Y1", "RSPO3", "RUNX3", "RXRA", "RXRB", "RYK", "RYR2", "S100A10", 
"S100A2", "S100A4", "S100A6", "S100A8", "S100A9", "S100B", "S100P", 
"SAA1/2", "SAT1", "SCG5", "SCGB3A1", "SEC23A", "SEC61G", "SELENOP", 
"SELL", "SELPLG", "SERPINA1", "SERPINA3", "SERPINB5", "SERPINH1", 
"SFN", "SH3BGRL3", "SIGIRR", "SIGLEC6", "SLC2A1", "SLC40A1", 
"SLPI", "SMAD2", "SMAD3", "SMAD4", "SMARCB1", "SMO", "SNAI1", 
"SNAI2", "SOD1", "SOD2", "SORBS1", "SOSTDC1", "SOX2", "SOX4", 
"SOX9", "SPARCL1", "SPINK1", "SPOCK2", "SPP1", "SPRY2", "SPRY4", 
"SQSTM1", "SRC", "SREBF1", "SRGN", "SST", "ST6GAL1", "ST6GALNAC3", 
"STAT1", "STAT3", "STAT4", "STAT5A", "STAT5B", "STAT6", "STMN1", 
"SYK", "TACSTD2", "TAGLN", "TAP1", "TAP2", "TBX21", "TCAP", "TCF7", 
"TCL1A", "TEK", "TFEB", "TGFB1", "TGFB2", "TGFB3", "TGFBR1", 
"TGFBR2", "THBS1", "THBS2", "THSD4", "TIE1", "TIGIT", "TIMP1", 
"TLR1", "TLR2", "TLR3", "TLR4", "TLR5", "TLR7", "TLR8", "TM4SF1", 
"TNF", "TNFAIP6", "TNFRSF10A", "TNFRSF10B", "TNFRSF10D", "TNFRSF11A", 
"TNFRSF11B", "TNFRSF12A", "TNFRSF13B", "TNFRSF13C", "TNFRSF14", 
"TNFRSF17", "TNFRSF18", "TNFRSF19", "TNFRSF1A", "TNFRSF1B", "TNFRSF21", 
"TNFRSF4", "TNFRSF9", "TNFSF10", "TNFSF12", "TNFSF13B", "TNFSF14", 
"TNFSF15", "TNFSF4", "TNFSF8", "TNFSF9", "TNNC1", "TNNT2", "TNXA/B", 
"TOP2A", "TOX", "TP53", "TPM1", "TPM2", "TPSAB1/B2", "TPT1", 
"TRDC", "TREM1", "TREM2", "TRGC1/2", "TSC22D1", "TSHZ2", "TSLP", 
"TSLPR", "TTN", "TTR", "TUBB", "TUBB4B", "TWIST1", "TWIST2", 
"TXK", "TYK2", "TYMS", "TYROBP", "UBA52", "UBE2C", "UPK3A", "VCAM1", 
"VCAN", "VDR", "VEGFA", "VEGFB", "VEGFC", "VEGFD", "VHL", "VIM", 
"VPREB3", "VSIR", "VTN", "VWA1", "VWF", "WIF1", "WNT10B", "WNT11", 
"WNT3", "WNT5A", "WNT5B", "WNT7A", "WNT7B", "WNT9A", "XBP1", 
"XCL1/2", "XKR4", "YBX3", "YES1", "ZBTB16", "ZFP36")
# PseudotimeDE::plotUncertainty(dm_results %>% select(merge_ID, df_time) %>% rename("cell" = "merge_ID", "pseudotime" = "df_time"), sub_tbl)

exp <- new("dgCMatrix", i = c(0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 
1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 
2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 
0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 
1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 
2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 
0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 
1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 
2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 
0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 
1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 
2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 
0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 
1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 
2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 
0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 
1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 
2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 
0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 
1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 
2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 
0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 
1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 
2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 
0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 
1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 
2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 
0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 
1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 
2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 
0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 
1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 
2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 
0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 
1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 
2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 
0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 
1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L), p = c(0L, 
3L, 6L, 9L, 12L, 15L, 18L, 21L, 24L, 27L, 30L, 33L, 36L, 39L, 
42L, 45L, 48L, 51L, 54L, 57L, 60L, 63L, 66L, 69L, 72L, 75L, 78L, 
81L, 84L, 87L, 90L, 93L, 96L, 99L, 102L, 105L, 108L, 111L, 114L, 
117L, 120L, 123L, 126L, 129L, 132L, 135L, 138L, 141L, 144L, 147L, 
150L, 153L, 156L, 159L, 162L, 165L, 168L, 171L, 174L, 177L, 180L, 
183L, 186L, 189L, 192L, 195L, 198L, 201L, 204L, 207L, 210L, 213L, 
216L, 219L, 222L, 225L, 228L, 231L, 234L, 237L, 240L, 243L, 246L, 
249L, 252L, 255L, 258L, 261L, 264L, 267L, 270L, 273L, 276L, 279L, 
282L, 285L, 288L, 291L, 294L, 297L, 300L, 303L, 306L, 309L, 312L, 
315L, 318L, 321L, 324L, 327L, 330L, 333L, 336L, 339L, 342L, 345L, 
348L, 351L, 354L, 357L, 360L, 363L, 366L, 369L, 372L, 375L, 378L, 
381L, 384L, 387L, 390L, 393L, 396L, 399L, 402L, 405L, 408L, 411L, 
414L, 417L, 420L, 423L, 426L, 429L, 432L, 435L, 438L, 441L, 444L, 
447L, 450L, 453L, 456L, 459L, 462L, 465L, 468L, 471L, 474L, 477L, 
480L, 483L, 486L, 489L, 492L, 495L, 498L, 501L, 504L, 507L, 510L, 
513L, 516L, 519L, 522L, 525L, 528L, 531L, 534L, 537L, 540L, 543L, 
546L, 549L, 552L, 555L, 558L, 561L, 564L, 567L, 570L, 573L, 576L, 
579L, 582L, 585L, 588L, 591L, 594L, 597L, 600L), Dim = c(3L, 
200L), Dimnames = list(c("AATK", "ABL1", "ABL2"), c("Cx05_S0_c_1_45_670", 
"Cx05_S1_c_2_275_278", "Cx05_S1_c_2_37_110", "Cx06_S1_c_2_32_999", 
"Cx05_S2_c_3_60_47", "Cx06_S0_c_1_105_149", "Cx05_S3_c_4_164_130", 
"Cx05_S3_c_4_122_708", "Cx06_S0_c_1_100_696", "Cx06_S0_c_1_93_1224", 
"Cx06_S0_c_1_46_818", "Cx05_S1_c_2_64_108", "Cx06_S3_c_4_6_766", 
"Cx05_S3_c_4_211_508", "Cx05_S2_c_3_94_363", "Cx05_S3_c_4_299_356", 
"Cx05_S2_c_3_71_204", "Cx05_S1_c_2_159_1106", "Cx06_S0_c_1_36_692", 
"Cx05_S3_c_4_105_278", "Cx05_S3_c_4_156_250", "Cx06_S0_c_1_126_1608", 
"Cx06_S0_c_1_26_677", "Cx05_S2_c_3_42_687", "Cx05_S3_c_4_66_247", 
"Cx06_S2_c_3_33_1272", "Cx06_S0_c_1_108_536", "Cx05_S3_c_4_42_41", 
"Cx06_S0_c_1_129_2098", "Cx05_S1_c_2_67_139", "Cx05_S3_c_4_32_1159", 
"Cx06_S0_c_1_16_2056", "Cx06_S2_c_3_101_287", "Cx05_S1_c_2_235_478", 
"Cx05_S2_c_3_87_1032", "Cx06_S0_c_1_76_303", "Cx06_S0_c_1_122_842", 
"Cx05_S0_c_1_25_152", "Cx05_S2_c_3_12_1213", "Cx06_S1_c_2_91_536", 
"Cx05_S1_c_2_150_40", "Cx06_S1_c_2_73_764", "Cx05_S3_c_4_185_832", 
"Cx05_S3_c_4_269_357", "Cx05_S1_c_2_174_443", "Cx06_S0_c_1_104_930", 
"Cx06_S2_c_3_90_380", "Cx05_S3_c_4_196_274", "Cx05_S3_c_4_27_238", 
"Cx05_S2_c_3_72_384", "Cx06_S2_c_3_140_782", "Cx06_S2_c_3_147_368", 
"Cx06_S3_c_4_90_235", "Cx05_S2_c_3_2_115", "Cx06_S2_c_3_80_776", 
"Cx05_S2_c_3_95_476", "Cx06_S3_c_4_22_1761", "Cx06_S2_c_3_54_210", 
"Cx05_S3_c_4_45_225", "Cx05_S1_c_2_279_1386", "Cx05_S1_c_2_71_155", 
"Cx05_S3_c_4_42_77", "Cx05_S1_c_2_88_932", "Cx06_S2_c_3_37_749", 
"Cx05_S2_c_3_39_698", "Cx06_S2_c_3_26_720", "Cx05_S1_c_2_281_258", 
"Cx05_S3_c_4_118_74", "Cx05_S3_c_4_123_173", "Cx05_S0_c_1_70_264", 
"Cx06_S1_c_2_71_409", "Cx05_S3_c_4_265_307", "Cx05_S1_c_2_136_137", 
"Cx05_S3_c_4_255_331", "Cx05_S1_c_2_113_140", "Cx06_S2_c_3_101_606", 
"Cx06_S0_c_1_76_399", "Cx05_S3_c_4_24_132", "Cx05_S2_c_3_14_227", 
"Cx06_S0_c_1_11_1244", "Cx05_S1_c_2_146_1461", "Cx05_S1_c_2_114_656", 
"Cx05_S2_c_3_7_284", "Cx06_S2_c_3_26_585", "Cx05_S2_c_3_47_336", 
"Cx05_S3_c_4_145_317", "Cx06_S2_c_3_124_813", "Cx06_S3_c_4_22_319", 
"Cx06_S3_c_4_86_1570", "Cx06_S3_c_4_24_1137", "Cx05_S0_c_1_81_385", 
"Cx06_S0_c_1_118_112", "Cx06_S2_c_3_61_1609", "Cx05_S1_c_2_76_469", 
"Cx06_S0_c_1_110_76", "Cx05_S1_c_2_284_697", "Cx06_S2_c_3_49_565", 
"Cx05_S2_c_3_20_324", "Cx05_S2_c_3_71_122", "Cx06_S3_c_4_85_1126", 
"Cx05_S1_c_2_183_396", "Cx05_S2_c_3_89_133", "Cx06_S0_c_1_10_2479", 
"Cx05_S3_c_4_45_591", "Cx05_S3_c_4_128_761", "Cx05_S3_c_4_61_919", 
"Cx05_S1_c_2_221_209", "Cx05_S0_c_1_8_749", "Cx06_S2_c_3_147_175", 
"Cx05_S3_c_4_104_11", "Cx05_S3_c_4_84_104", "Cx06_S0_c_1_27_338", 
"Cx05_S1_c_2_185_506", "Cx06_S2_c_3_113_745", "Cx05_S0_c_1_78_384", 
"Cx06_S1_c_2_25_1217", "Cx06_S0_c_1_29_442", "Cx06_S0_c_1_28_789", 
"Cx06_S2_c_3_71_1078", "Cx05_S1_c_2_192_553", "Cx06_S3_c_4_79_564", 
"Cx05_S0_c_1_84_200", "Cx05_S3_c_4_192_1171", "Cx05_S0_c_1_43_209", 
"Cx05_S3_c_4_181_68", "Cx05_S1_c_2_131_36", "Cx06_S0_c_1_9_1272", 
"Cx05_S0_c_1_46_806", "Cx05_S1_c_2_98_954", "Cx05_S3_c_4_269_523", 
"Cx05_S1_c_2_89_524", "Cx06_S1_c_2_26_201", "Cx05_S3_c_4_217_211", 
"Cx06_S0_c_1_63_559", "Cx06_S0_c_1_6_3174", "Cx06_S0_c_1_80_678", 
"Cx05_S1_c_2_266_440", "Cx05_S0_c_1_66_201", "Cx06_S0_c_1_5_1199", 
"Cx06_S1_c_2_65_737", "Cx05_S1_c_2_264_589", "Cx06_S2_c_3_12_1892", 
"Cx06_S0_c_1_66_34", "Cx05_S3_c_4_52_774", "Cx05_S1_c_2_95_489", 
"Cx06_S2_c_3_126_429", "Cx05_S1_c_2_219_209", "Cx05_S1_c_2_81_838", 
"Cx06_S0_c_1_9_765", "Cx06_S1_c_2_38_1121", "Cx06_S2_c_3_4_375", 
"Cx05_S3_c_4_114_84", "Cx06_S2_c_3_71_102", "Cx05_S3_c_4_95_99", 
"Cx06_S2_c_3_54_889", "Cx05_S3_c_4_85_559", "Cx05_S1_c_2_108_353", 
"Cx05_S0_c_1_9_435", "Cx05_S1_c_2_186_120", "Cx05_S1_c_2_206_154", 
"Cx05_S1_c_2_81_198", "Cx06_S2_c_3_68_653", "Cx05_S2_c_3_33_162", 
"Cx06_S2_c_3_75_1174", "Cx05_S2_c_3_77_112", "Cx06_S3_c_4_2_290", 
"Cx06_S2_c_3_114_627", "Cx06_S0_c_1_18_3344", "Cx06_S0_c_1_121_2259", 
"Cx05_S1_c_2_143_829", "Cx05_S3_c_4_292_213", "Cx06_S0_c_1_93_692", 
"Cx06_S2_c_3_3_1445", "Cx05_S1_c_2_97_52", "Cx06_S2_c_3_142_730", 
"Cx06_S0_c_1_1_594", "Cx06_S0_c_1_17_1115", "Cx06_S2_c_3_63_722", 
"Cx05_S1_c_2_201_478", "Cx05_S2_c_3_66_691", "Cx05_S3_c_4_196_122", 
"Cx05_S0_c_1_17_289", "Cx05_S3_c_4_282_532", "Cx05_S0_c_1_73_167", 
"Cx05_S2_c_3_38_556", "Cx06_S0_c_1_16_208", "Cx05_S3_c_4_138_532", 
"Cx05_S0_c_1_15_9", "Cx05_S2_c_3_17_630", "Cx05_S1_c_2_110_269", 
"Cx05_S3_c_4_262_554", "Cx06_S0_c_1_2_534", "Cx05_S1_c_2_155_684", 
"Cx06_S2_c_3_52_736", "Cx06_S3_c_4_3_673", "Cx06_S2_c_3_25_2179", 
"Cx05_S3_c_4_13_768", "Cx05_S2_c_3_56_648", "Cx06_S1_c_2_47_926", 
"Cx05_S1_c_2_204_635")), x = c(1.75153985029218, 1.91209951523177, 
1.90462555045384, 1.56590195697459, 1.85466843089818, 1.82158964639396, 
1.73025927675103, 2.36311332227666, 2.00954807593711, 0.978378815056369, 
2.02149987946733, 1.06383880361079, 2.40545133487426, 1.86540738835215, 
1.68613902635075, 1.54653589195984, 2.06460237205783, 1.69861669583311, 
2.26229987463514, 2.20903998592273, 1.97489821007904, 2.14028617303242, 
2.31816863277618, 2.18444791622278, 0.990689010418363, 2.43133449269122, 
2.09204395218098, 1.57279820885965, 1.89946248816174, 1.4536361134338, 
0.89436481888818, 1.21088638820222, 1.09556327968863, 1.8495182475491, 
2.01528584938192, 1.72850598280765, 1.80339115017311, 1.49025650584313, 
1.3248479745422, 1.5893778295045, 2.08083135112905, 1.74788002132184, 
1.22461281557875, 2.17687669641087, 1.9813427726303, 2.26197655211883, 
2.04867359117046, 1.6224742418696, 1.2475785153474, 2.3680773499314, 
1.65115508034667, 1.64824116511358, 1.86350566721822, 1.7254750798845, 
1.36452074658013, 2.35256934254892, 1.76343358329027, 1.35794348162395, 
1.33332365584153, 1.33101865553108, 1.69094882884152, 2.2043924463661, 
2.58585145676655, 1.13557316552135, 2.05192416342562, 1.48419261838412, 
1.20126818005317, 1.99219346301259, 1.22482589755705, 1.72094416858844, 
2.28798796135722, 1.85913552570335, 1.53031224731699, 1.48040470092525, 
1.54026754287192, 1.53687546617661, 2.02085994671616, 1.64762902412133, 
1.36238973256164, 2.11266744412964, 1.8567288001143, 2.07756692915998, 
2.14485270397424, 1.94020433646378, 1.46325328217367, 1.93457232509749, 
1.92154074730694, 1.30460231013287, 2.13707461250406, 1.70950317132062, 
2.6366207320712, 2.46464841643144, 2.02552072848708, 1.51541836295498, 
2.1967189063418, 1.88089042977249, 1.15845877065033, 1.84185253175872, 
1.51246800301857, 1.09088529678331, 2.20079730375684, 1.62346649512618, 
0.965781588823284, 1.69366793657247, 1.98972441897789, 1.11012818217199, 
1.49077845900762, 1.12360904064752, 2.18076360729309, 2.43494657117543, 
2.2396019595044, 2.30336900641469, 2.17525306859066, 1.49779365692194, 
1.73930790140364, 1.93631407390737, 1.46738935307144, 2.10669797881385, 
2.77348343430186, 2.11956592142892, 2.30396399074441, 2.38236646839554, 
2.2600536824078, 1.6257071128226, 2.61665905731098, 2.03255160656869, 
1.81019479543164, 1.99441878610116, 1.1782304876772, 1.79407902099207, 
1.87316024537535, 1.8149963777911, 2.06401196271908, 2.06212691072755, 
1.80356717622695, 0.642020847075001, 1.49250327476295, 1.28322524259704, 
1.93156149128672, 2.24574454951323, 2.03606647632131, 2.33270166131251, 
2.36706322314807, 1.87813960697492, 1.15469702138315, 1.34430618981318, 
1.29156870498271, 1.61765739872065, 2.67870008426878, 1.89560570624297, 
1.17383853958375, 1.85899369991791, 1.38171409549059, 0.929910957048374, 
1.27765768865938, 1.34452933897627, 1.46381684915204, 2.06410456571098, 
1.51963761200844, 1.8395750080409, 1.91933370946526, 2.35799028762508, 
0.74729765335517, 0.835824161034001, 0.878172713525334, 1.80003953796236, 
1.89782899062662, 1.95566462153173, 0.940959777937523, 1.55218399917263, 
1.32181070737398, 0.790321203654451, 1.65444450603752, 1.16066443931422, 
2.1110322486106, 2.41975135527024, 2.15055652402872, 2.02128746176296, 
2.18864794110756, 2.08558676930084, 1.4351242856949, 1.89069899218998, 
1.67491870580118, 3.45473384711813, 2.14052613228323, 0.951147459719627, 
2.26692139181442, 2.13148547328642, 1.86477213729924, 1.70211340455437, 
1.86962619632262, 1.87373340599134, 1.29344071085328, 2.32214351528564, 
1.69546434502416, 1.37037739956757, 1.44214982306015, 1.5437415413354, 
1.73890046917187, 1.96865311947728, 1.75198562473517, 1.76429607700516, 
2.14127912589267, 2.05010103994565, 1.9501821666812, 2.16380167216172, 
1.92598538487415, 1.16570307017815, 2.21148331459327, 1.56442970069988, 
2.44302799448886, 2.54359798438875, 1.70243354385792, 2.23234252849371, 
2.19944077614683, 1.51579447139636, 2.13328700068037, 2.16596932084542, 
2.0446954203141, 0.90947632831714, 1.27981379558657, 1.16817711693582, 
1.52816342430037, 1.85791312073768, 1.68026168704264, 1.22136182116847, 
1.94601678965359, 1.40802678554355, 1.40724595493721, 1.85671350245478, 
1.83427071016311, 1.63896819859787, 1.6669323911142, 1.71451838447725, 
1.97182267235425, 2.56575259175452, 1.28281505389738, 1.36589483873775, 
1.69262316488005, 1.06159498968317, 2.22749721289136, 2.32529010187384, 
1.80995910535943, 1.63686359080377, 1.77447448977234, 1.46046335313018, 
1.75214433565673, 2.20666165766988, 1.62864956136211, 1.29549776833785, 
1.89827755450233, 1.62918225158435, 2.17940673449057, 1.77734379795, 
1.49202871420333, 1.45417454449016, 1.53386755525991, 1.33392597157059, 
2.12817845280214, 2.30737527069215, 1.76231675184137, 1.36012208320673, 
1.59080797648379, 1.1887364510079, 2.01836771685287, 1.93294675801674, 
1.16831632339414, 1.53374545316451, 1.81499355008455, 1.64289769449839, 
1.92644706106437, 2.57222880241467, 1.59396023919526, 2.01245697776762, 
1.87471042100742, 1.87564488804621, 1.82060083246011, 1.79216399895331, 
1.83434562279477, 0.932700263561167, 1.65148766299728, 1.34069375075404, 
1.6856165792477, 1.91762133951985, 1.63481887921343, 1.62700222722352, 
1.71269020809702, 1.6278801928721, 1.88081665470954, 1.9063804315067, 
1.84218955713602, 0.971141628481282, 1.40582829129155, 1.28669781018652, 
2.02121683428216, 2.42157384800937, 2.18480844987205, 1.73734560416536, 
2.19161296872195, 1.90299709896122, 2.23290194477688, 2.10466039350341, 
2.02782491275839, 1.43968447760872, 2.17569627503847, 1.47674085178935, 
1.29374319582761, 2.03551109931116, 1.90343882575745, 1.97810126333201, 
1.85075368474609, 1.85198843064272, 1.76793621804676, 1.66184623264352, 
1.55802831316857, 1.75751426047623, 2.09892150383661, 3.14403132017283, 
1.91638915415631, 2.29905547928254, 1.80037113271217, 1.48117623773955, 
2.41306142647072, 1.98206109211961, 1.70649928500607, 2.18442427964042, 
1.9673418123533, 2.55956543310763, 2.29220863773449, 1.16568767041536, 
2.38493619663519, 2.16382329694649, 1.82393801368085, 1.21683480214439, 
2.12798620428292, 1.59905623586206, 1.94924140668134, 2.13919482458481, 
1.79525889274913, 1.84077522553472, 2.28911123769921, 1.91040504716865, 
1.98538478589685, 2.30055841284274, 1.69131786627364, 1.23045779065418, 
2.07816854658762, 1.73436487975558, 1.18503394046283, 2.085189884399, 
1.77384696080912, 1.38745525014524, 1.63255384722168, 1.31198724846973, 
0.976439996221428, 1.45795374733814, 1.33365232824834, 1.95557189664352, 
1.82714847272395, 1.71642914242906, 1.41980836690647, 2.47430542171958, 
1.69779938243199, 1.25258777747212, 2.4919593099716, 1.98541588722853, 
0.973604414858916, 1.28423385036537, 1.00120104600339, 2.358969040694, 
2.41640714967589, 1.9315210051707, 2.60521858486031, 2.41433964659149, 
1.83503579985977, 2.04779934844271, 1.9755554650617, 1.83018921857536, 
0.667159212052591, 1.71724533290737, 1.29974774961684, 0.69437867757286, 
2.05912541810894, 1.37033651650606, 2.10577984255499, 2.05242104577976, 
1.89623504142852, 1.24723690756069, 1.14995947187836, 1.19962338335463, 
1.57975230492202, 1.8596418701055, 1.69543473388593, 1.62925296904878, 
2.15143742581256, 1.90307398401675, 1.0596788589833, 1.4379165137425, 
1.03998135234864, 2.0654665167502, 2.46535871039494, 2.1719841461353, 
0.286658538507844, 0.907784759811373, 0.77356795892303, 0.483443414402982, 
1.039895056347, 1.18983296628073, 2.29004235308136, 2.35328933755861, 
2.21402804761125, 1.36169208825568, 2.20350743638574, 1.60472590333943, 
0.569348460873072, 2.51602469711153, 1.99711676979763, 1.78678313727548, 
2.64437356484108, 1.90812624509756, 1.7896909273975, 1.96042023266985, 
1.98559789243378, 1.31718625438325, 1.37232129376045, 1.29383896604805, 
1.16656993794703, 1.38854678823575, 1.18141951240098, 2.43665660501433, 
2.25378842130415, 2.39083344160787, 2.2190066821269, 2.23984557553909, 
2.1206172736364, 2.43213786963714, 2.23166300499897, 1.56461764491307, 
1.80835075744811, 1.87472719824772, 1.72946484758112, 1.94428669904928, 
1.94247325035016, 1.94128081129888, 0.871412688376694, 1.79824089903502, 
1.57986473222311, 1.7209053162782, 2.74467957795223, 1.76125293372571, 
1.34616626864155, 1.65593261559163, 1.61930405906282, 1.50036471251679, 
2.10090431420041, 1.64654325581492, 1.14144660083756, 1.8924281425254, 
1.48680180128455, 1.75766457654881, 1.88355941962066, 1.8980135235339, 
0.651692731253312, 1.47519761011826, 1.0242623800327, 2.01200227222988, 
2.27420495140909, 2.05838737162112, 2.24089426265409, 2.36432256618822, 
2.2233367299897, 1.93128734394698, 2.32899359358275, 2.15873294051565, 
1.45678386646928, 1.76334220204838, 1.47637225562316, 2.03019540623591, 
2.06426088097047, 1.73509543314658, 2.07817188550336, 1.99536323128311, 
1.85212395973821, 0.80356084451512, 1.64097256509284, 1.20088248215088, 
2.07463012112441, 1.5198650980505, 1.31214146947478, 1.46289241409735, 
1.7338746863821, 1.50031496559527, 2.08039610629288, 2.19575483861573, 
1.34920844446497, 1.90644819822091, 1.40646612078342, 1.20773097817952, 
2.09830899382266, 2.26655420272358, 2.16777922902782, 0.774285880812297, 
1.28462865249836, 1.24615298423764, 2.20740339038715, 2.34592871235146, 
2.03440419653844, 1.66985940703767, 2.02350012101497, 1.78912521782319, 
0.336490416551723, 0.825516068073956, 0.483170353576858, 0.819537168151227, 
1.40314837908957, 1.47882989041189, 1.52613284080165, 1.78745904249775, 
1.50620174206122, 1.98202399248294, 2.06975127872821, 1.92752564616381, 
2.02253431602661, 2.23574825041869, 2.05082350840064, 0.893359531396041, 
1.85362084460776, 1.31609603287658, 0.71690194796631, 1.33588142428831, 
0.803136135226853, 1.12482210440761, 1.69371549073889, 1.49545363386938, 
1.92467913128523, 2.13219145013739, 1.80728584819998, 1.80800511104066, 
2.56462168900206, 1.52201580901126, 2.66896343502036, 2.11221590131541, 
1.46618344167959, 2.62927662255403, 1.89139449655174, 1.64802891927017, 
2.4502157842764, 2.21767118302864, 1.49701474377011, 2.10301301285356, 
2.64894249356849, 1.50083707237937, 1.70013970768701, 2.00298500859266, 
1.34405592284147, 0.71923954911812, 1.36751956776982, 1.56001481395469, 
2.07254907755874, 2.05302638949275, 1.74964226007326, 1.72705413521355, 
2.12210452656029, 1.76732304151593, 1.47993496061864, 1.75885059232323, 
1.71192352210111, 2.22249926435764, 2.22490535692473, 2.09419449596379, 
0.946321357105801, 1.27406833074601, 1.43496672418478, 0.752760038116481, 
1.78043187512046, 1.60926938003069, 1.26503033526995, 1.73301841944999, 
1.36482026756594, 0.411504297510352, 1.48493509742712, 0.777087713029433, 
2.22416577218628, 2.05142147477861, 2.1254201162964, 0.937141823364205, 
1.70390069448719, 1.4987652188182, 0.749259046028163, 1.18790701346676, 
1.02694717273448, 0.952505754259787, 1.12143707302238, 0.904803061139261, 
1.61842870080033, 2.77784975931466, 2.33562749108646, 1.52358133330614, 
2.14568459641795, 1.71050698891479), factors = list())

lapply(sub_tbl_test, function(x) all(x[["cell"]] %in% orig_tbl_test$cell)) # are all sub in orig?

system.time(res <- PseudotimeDE::runPseudotimeDE(gene.vec = gene.vec,
                                     ori.tbl = orig_tbl_test,
                                     sub.tbl = sub_tbl_test, 
                                     mat = exp, 
                                     model = "nb",
                                     mc.cores = 50))
Error in PseudotimeDE::runPseudotimeDE(gene.vec = gene.vec, ori.tbl = orig_tbl_test,  : 
  Some cells in sub.tbl are not a subset of ori.tbl
Timing stopped at: 0.005 0 0.005
SONGDONGYUAN1994 commented 1 year ago

@mcaponegro Hi I actually run your code here and surprisingly I can run it and does not return an error. That is super weird. Did you re-start R after re-installing? If it still does not work, let us schedule a meeting. You can email me dongyuansong@ucla.edu. Thanks!