Error in library(TCGA2STAT) : there is no package called ‘TCGA2STAT’ In addition: Warning message: replacing previous import ‘AUCell::cbind’ by ‘SingleCellExperiment::cbind’ when loading ‘SCENIC’ [1] "UCECHs3" Warning: The 'show_progress' argument is deprecated as of v0.3. Use 'verbosity' instead. (in sctransform::vst) Calculating cell attributes from input UMI matrix: log_umi Variance stabilizing transformation of count matrix of size 16234 by 1351 Model formula is y ~ log_umi Get Negative Binomial regression parameters per gene Using 2000 genes, 1351 cells | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% Found 81 outliers - those will be ignored in fitting/regularization step Second step: Get residuals using fitted parameters for 16234 genes | | | 0% | |== | 3% | |==== | 6% | |====== | 9% | |======== | 12% | |=========== | 15% | |============= | 18% | |=============== | 21% | |================= | 24% | |=================== | 27% | |===================== | 30% | |======================= | 33% | |========================= | 36% | |============================ | 39% | |============================== | 42% | 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|==================================================================== | 97% | |======================================================================| 100% Computing corrected count matrix for 16234 genes | | | 0% | |== | 3% | |==== | 6% | |====== | 9% | |======== | 12% | |=========== | 15% | |============= | 18% | |=============== | 21% | |================= | 24% | |=================== | 27% | |===================== | 30% | |======================= | 33% | |========================= | 36% | |============================ | 39% | |============================== | 42% | |================================ | 45% | |================================== | 48% | |==================================== | 52% | |====================================== | 55% | |======================================== | 58% | |========================================== | 61% | |============================================= | 64% | |=============================================== | 67% | 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default assay to SCT There were 50 or more warnings (use warnings() to see the first 50) PC_ 1 Positive: COL3A1, MGP, MMP11, IGFBP7, LUM, TAGLN, COL6A1, DCN, COL6A2, SPARC MMP2, TIMP1, COL1A1, ECM1, APCDD1, COL1A2, MYL9, AEBP1, BGN, VIM LGALS1, ACTA2, ISLR, IGFBP4, SPARCL1, A2M, FBLN1, IFITM3, COL7A1, PDGFRB Negative: CD24, WFDC2, PIGR, C3, ELF3, LGR5, LCN2, PAX8, EPCAM, MUC1 MMP7, SLPI, ASRGL1, HMGCR, TACSTD2, GABRP, ANXA2, SPINT2, LRIG1, KRT19 SOX17, MSLN, ADAMTS1, TMEM101, THSD4, GRIA2, ID1, CCDC6, RHEX, CLDN3 PC_ 2 Positive: STMN1, COX7C, HMGN2, S100A4, NACA, ID3, SRP14, MDK, BCAT1, MT1E EEF1A1, FAU, MT1F, TPT1, MYL6, MFAP2, HINT1, UBA52, TUBA1A, HPGD FTL, TUBA1B, TMSB10, PPA1, C19orf33, H2AFZ, ID1, AGTR2, UPK1B, GRIA2 Negative: C3, PIGR, LCN2, FOS, ELF3, SAT1, SLC40A1, ZFP36, SLPI, CD74 PDZK1IP1, TCIM, GABRP, FAM20A, IGFBP3, TNFAIP2, NCOA7, SAA1, SPP1, CXCL5 SOD2, AC009501.1, VMP1, CACNA1A, MUC4, PGGHG, MMP7, SLC34A2, DDIT4, ATF3 PC_ 3 Positive: CACNA1A, A2M, EGFL7, AC009501.1, COL4A1, VWF, KCNJ3, ZNF302, MCAM, CD34 PECAM1, LGR5, RAMP2, FN1, GRIA2, GREM1, SPARC, AQP1, COL4A2, CLEC14A ADGRL4, CALCRL, TIMP3, IGFBP4, IGFBP7, CD93, ESAM, MALAT1, FOXP1, RGS5 Negative: IGLC2, IGKC, IGHG1, IGHG3, MMP7, IGHGP, IGLC3, IGHG2, IGHA1, JCHAIN IGHG4, FOS, IGHM, FABP5, MZB1, C3, SLPI, EGR1, CTSB, TMSB4X DCN, IFITM3, BTG2, WFDC2, IER3, TPT1, NR4A1, MMP2, IFITM1, LY6D PC_ 4 Positive: FOS, COL4A1, FN1, A2M, NR4A1, SPARC, ZFP36, MCAM, DUSP1, RAMP2 COL4A2, EGR1, MMP7, EPAS1, ACTA2, CTGF, AQP1, CD93, CLEC14A, VWF ADIRF, ENG, MYL9, EGFL7, IFITM2, RGS5, CD34, S100A4, ENPP2, ATF3 Negative: CACNA1A, COL7A1, AC009501.1, CCL21, FBLN1, NBL1, PGGHG, GPX3, CCNL2, COL6A1 COL16A1, ZNF302, KCNJ3, TRBC2, MMP11, GREM1, PLXNB1, LRP1, CD52, ECM1 PAX8, CCL5, MXRA8, LSP1, XIST, MAN2C1, TCIRG1, PTPN7, SLC25A37, DCN PC_ 5 Positive: IGKC, IGLC2, CACNA1A, IGHG1, IGHG3, AC009501.1, IGLC3, IGHGP, KCNJ3, ZNF302 IGHG2, IGHA1, ELF3, PGGHG, PAX8, NR4A1, GREM1, FOXP1, LGR5, IGHG4 PLXNB1, CXCL14, AL035078.1, AD000090.1, GRIA2, XIST, AC007952.4, TSPAN3, IGHM, LRRC69 Negative: CD74, FTL, SLPI, B2M, HLA-DRB1, MMP7, SAA1, TPT1, HLA-DPA1, HLA-DRA SAA2, RARRES3, WFDC2, NACA, HLA-B, TMSB10, LCN2, S100A4, C3, FAU S100A6, C1QB, APOC1, HINT1, CCL21, HLA-DPB1, TYROBP, C1orf194, UBA52, CD52 Warning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation' This message will be shown once per session 10:10:18 UMAP embedding parameters a = 0.9922 b = 1.112 10:10:18 Read 1351 rows and found 10 numeric columns 10:10:18 Using Annoy for neighbor search, n_neighbors = 30 10:10:18 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 10:10:19 Writing NN index file to temp file /tmp/Rtmpx9LZSv/file3896572721996 10:10:19 Searching Annoy index using 1 thread, search_k = 3000 10:10:19 Annoy recall = 100% 10:10:20 Commencing smooth kNN distance calibration using 1 thread 10:10:21 Initializing from normalized Laplacian + noise 10:10:21 Commencing optimization for 500 epochs, with 54154 positive edges 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 10:10:28 Optimization finished null device 1 Computing nearest neighbor graph Computing SNN Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 1351 Number of edges: 44962 Running Louvain algorithm... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.7455 Number of communities: 9 Elapsed time: 0 seconds [1] 3000 1351 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 5 6 7 8 9 10 11 11 10 13 12 14 13 14 17 14 18 16 17 21 17 [1] "11" $m_C3 [1] "C3" "PIGR" "LCN2" "FOS" "MMP7" "SLPI" [7] "PDZK1IP1" "ATF3" "CXCL3" "CXCL5" "TCIM" "ZFP36" [13] "NCOA7" "ELF3" "SLC40A1" "DDIT4" "SOD2" "WFDC2" [19] "CCL20" "CXCL1" "GABRP" "CRISP3" "BHLHE40" "RDH10" [25] "NR4A1" "BTG2" "MUC4" "CEACAM7" "ZC3H12A" "SAT1" [31] "CFB" "APOL1" "IL4I1" "MUC5B" "SPP1" "DEFB1" [37] "C4BPA" "GDF15" "IDO1" "TRIM31" "SLC34A2" "CXCL8" [43] "ATP1B1" "SERPINA1" "SEMA4B" "VEGFA" "HLA-DRA" "XBP1" [49] "C2CD4A" "SOCS3" "IER3" "NDRG1" "MUC16" "PLEKHS1" $m_MS4A8 [1] "MS4A8" "TPPP3" "CFAP157" "SAA1" "C1orf194" [6] "RSPH1" "SAA2" "CCDC78" "EFHC1" "BAIAP3" [11] "DNAAF1" "CCNO" "FOXJ1" "DLEC1" "VWA3A" [16] "FAM183A" "CROCC2" "CFAP43" "C20orf85" "CFAP70" [21] "C5orf49" "DNAI1" "CAPSL" "LEFTY1" "RRAD" [26] "C9orf24" "LRRC46" "CFAP100" "LRRC23" "CAPS" [31] "HIST1H1C" "DNAH12" "E2F7" "MAPK15" "CFAP73" [36] "CCDC187" "RARRES3" "MOK" "SCGB1D2" "CFAP45" [41] "EFCAB1" "CDHR4" "OMG" "CDHR3" "RFX2" [46] "HGFAC" "SCGB2A1" "TOGARAM2" "CCDC114" "AC007906.2" $m_COX7C [1] "COX7C" "HMGN2" "STMN1" "NACA" "S100A4" "SRP14" [7] "HPGD" "BCAT1" "ID3" "MT1F" "UPK1B" "HINT1" [13] "MDK" "MT1E" "AGTR2" "TPT1" "H2AFZ" "HSPA5" [19] "PPA1" "S100A10" "C19orf33" "TUBA1A" "ID1" "TUBA1B" [25] "KIAA1324" "MFAP2" "FBN2" "GRIA2" "COL12A1" "EEF1A1" [31] "AGR2" "IFI27" "F3" "RCN2" "CD24" "PXMP2" [37] "S100A2" "ARSJ" $m_LGR5 [1] "LGR5" "IFI6" "ZNF579" "NPY1R" "TSPAN3" [6] "GABPB1-AS1" "PIK3R1" "DCBLD2" "ZNF160" "PCSK4" [11] "SLC4A2" "SLC18B1" "CPNE8" "TOP2A" "AL390728.6" [16] "JUND" "CCDC6" "LGR4" "PTAR1" "HIC2" [21] "MCCC2" "GSR" $m_CACNA1A [1] "CACNA1A" "AC009501.1" "KCNJ3" "ZNF302" "GREM1" [6] "PGGHG" "PLXNB1" "SLC25A37" "FOXP1" "AL035078.1" [11] "PAX8" "AD000090.1" "LRRC69" "GLYCTK" "CXCL14" [16] "TNFAIP2" "COL18A1" "SLITRK5" "MUC1" "FILIP1" [21] "TMEM101" "MBD6" "SH3GLB2" "XIST" "INF2" [26] "EPS8L2" "ACADVL" "STAG2" "SFPQ" "SLC38A2" [31] "REC8" "CNDP2" "STX18" "CD47" "MSLN" $m_AGPAT5 [1] "AGPAT5" "CLIP4" "FOXK1" "CACTIN" "SLITRK4" [6] "TGDS" "MST1" "RGS1" "ISG15" "BICRA" [11] "NEK7" "ZBTB14" "FLCN" "SUGP2" "LPCAT2" [16] "MMP10" "RAC2" "INTU" "PRR5" "AC048341.1" [21] "WDR35" "CDH16" "SIGLEC1" "MED17" "CPNE7" [26] "C3orf58" "PANK3" "ZNF90" "SDF4" "HSPA13" [31] "IRF2BPL" "RARA-AS1" "LONRF2" "TUBGCP6" "HLA-DQA1" [36] "ATP5MGL" "SCMH1" "SHANK3" "SLCO2B1" "SFT2D2" [41] "MAFB" "PPARD" "MGAT4B" "RASSF4" "KLHDC1" [46] "CADM1" "TACC1" "TIMM22" "RBMS3" "C1QTNF9B" [51] "LMO4" $m_ELOB [1] "ELOB" "ACADS" "TSPYL2" "UBL5" "BCAR1" [6] "RBM6" "NISCH" "EEF1D" "NFKBIE" "PBXIP1" [11] "TMSB10" "WSB1" "SELENOO" "CISH" "VPS51" [16] "TAZ" "BRF1" "GDI1" "KCTD12" "HEMK1" [21] "EIF5AL1" "NEMP1" "ACBD4" "PDLIM7" "AC021097.1" [26] "TMEM259" "GGA1" "MVD" "CTSD" "VWA1" [31] "DVL3" "GRAP" "FAM193B" "ZBTB20" "INTS11" [36] "FAU" "DMAP1" "ARHGEF17" "CHKB" "MIGA1" [41] "MAP1LC3A" "S100A6" "UBR4" "NEUROD2" "GNAI2" [46] "MYL6" "CEP164" "SLC9A3R2" "PITPNM3" "CDK3" [51] "POLK" "GOLGA8B" "PHLDB1" "CLBA1" "PLAU" $m_COL3A1 [1] "COL3A1" "DCN" "MMP11" "COL6A2" "LUM" "COL6A1" "ECM1" "TAGLN" [9] "MGP" "MMP2" "APCDD1" "COL1A1" "LGALS1" "ISLR" "SPON2" "AEBP1" $m_CD52 [1] "CD52" "CCL21" "FTL" "C1QB" "TRBC1" "TRBC2" [7] "TYROBP" "CORO1A" "PTPRC" "C1QA" "LYZ" "LSP1" [13] "CD2" "HLA-DPA1" "LIMD2" "GMFG" $m_A2M [1] "A2M" "COL4A1" "VWF" "EGFL7" "FN1" "SPARC" "AQP1" [8] "PLVAP" "RGCC" "ENG" "IGFBP7" "COL4A2" "RAMP2" "CD34" [15] "MCAM" "PECAM1" "RGS5" "CD93" "VIM" "CLEC14A" "ESAM" [22] "TM4SF1" "EPAS1" "CALCRL" "PTPRB" "HOPX" "ADGRL4" "ENPP2" [29] "CTGF" "HOXD9" "KDR" "LMO2" "ADCY4" "FLT1" $m_IGKC [1] "IGKC" "IGLC2" "IGHG1" "IGHG3" "IGLC3" "IGHA1" "IGHGP" [8] "CLU" "IGHG2" "GPX3" "IGHG4" "IGHM" "JCHAIN" "SSR4" [15] "RARRES1" "MZB1" "TSPAN9" "HSPA1A" Warning message: Using `as.character()` on a quosure is deprecated as of rlang 0.3.0. Please use `as_label()` or `as_name()` instead. This warning is displayed once per session. null device 1 Calculating cluster 0 Calculating cluster 1 Calculating cluster 2 Calculating cluster 3 Calculating cluster 4 Calculating cluster 5 Calculating cluster 6 Calculating cluster 7 Calculating cluster 8 Warning message: CombinePlots is being deprecated. Plots should now be combined using the patchwork system. Calculating cluster m_C3 Calculating cluster m_MS4A8 Calculating cluster m_COX7C Calculating cluster m_LGR5 Calculating cluster m_CACNA1A Calculating cluster m_COL3A1 Calculating cluster m_CD52 Calculating cluster m_A2M Warning message: CombinePlots is being deprecated. Plots should now be combined using the patchwork system. null device 1