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] "GISTHs1" 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 15641 by 2624 Model formula is y ~ log_umi Get Negative Binomial regression parameters per gene Using 2000 genes, 2624 cells | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% Found 67 outliers - those will be ignored in fitting/regularization step Second step: Get residuals using fitted parameters for 15641 genes | | | 0% | |== | 3% | |==== | 6% | |======= | 9% | |========= | 12% | |=========== | 16% | |============= | 19% | |=============== | 22% | |================== | 25% | |==================== | 28% | |====================== | 31% | |======================== | 34% | |========================== | 38% | |============================ | 41% | |=============================== 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|==================================================================== | 97% | |======================================================================| 100% Computing corrected count matrix for 15641 genes | | | 0% | |== | 3% | |==== | 6% | |======= | 9% | |========= | 12% | |=========== | 16% | |============= | 19% | |=============== | 22% | |================== | 25% | |==================== | 28% | |====================== | 31% | |======================== | 34% | |========================== | 38% | |============================ | 41% | |=============================== | 44% | |================================= | 47% | |=================================== | 50% | |===================================== | 53% | |======================================= | 56% | |========================================== | 59% | |============================================ | 62% | |============================================== | 66% | |================================================ | 69% | 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PC_ 1 Positive: LYZ, MUC6, MSMB, AGR2, PIGR, AC020656.1, PGC, SPINK1, REG1A, TFF2 OLFM4, BPIFB1, MUC5AC, SERPINA1, CD24, S100P, KRT8, TFF1, KRT19, MUC1 TFF3, GKN1, TSPAN8, AKR1B10, GKN2, GP2, KRT18, MUCL3, FAM3D, CXCL17 Negative: TAGLN, DES, MYL9, TPM2, ACTG2, ACTA2, GREM1, CNN1, FLNA, MYH11 PPP1R14A, CSRP1, HSPB1, ELN, TPM1, CRYAB, AEBP1, COL3A1, PTGER1, IGFBP7 MYLK, LGALS1, SYNPO2, CALD1, COL1A1, COL1A2, FLNC, SPARC, ACTC1, FN1 PC_ 2 Positive: PLAT, LY6H, CTSL, ISLR, DPT, SFRP1, KCNK3, PENK, TIMP1, MGP A2M, FGL2, PDGFRA, GPX3, FXYD6, HSPB6, LY6E, LEFTY2, PSD, IGFBP5 CPE, MFAP4, AC008397.2, CD74, C7, HLA-DPA1, MALAT1, HLA-DPB1, PTP4A3, IFI6 Negative: TAGLN, DES, MUC6, MYL9, ACTG2, LYZ, TPM2, TFF2, MSMB, GREM1 PIGR, AC020656.1, AGR2, SPINK1, CNN1, ACTA2, PGC, REG1A, MYH11, BPIFB1 TFF3, FLNA, SERPINA1, OLFM4, MUC1, CD24, GP2, KRT19, PPP1R14A, KRT8 PC_ 3 Positive: AKR1B10, KRT19, GKN1, KRT8, GKN2, MUCL3, S100P, TFF1, LGALS4, MUC5AC PSCA, PHGR1, GPX2, FCGBP, IL1R2, LINC01133, RFLNA, JPT1, KRT18, IFI27 C19orf33, CAPN8, CTSE, ANXA10, TMEM54, SDCBP2, S100A14, PLAC8, EPS8L1, VILL Negative: MUC6, LYZ, PIGR, PGC, BPIFB1, REG1A, SERPINA1, MSMB, GP2, OLFM4 AC020656.1, TFF2, TFF3, AQP5, FAM3D, AC139749.1, LTF, TCN1, ZG16B, LIPF C6orf58, CXCL17, REG3A, CLDN2, PDIA2, GAST, LCN2, KCNN4, A4GNT, SPINK1 PC_ 4 Positive: FN1, VWF, SERPINE1, COL1A1, CTGF, PECAM1, IGFBP7, AQP1, S100A4, ZFP36 COL4A1, FOS, DEPP1, IGKC, POSTN, CDH5, ADIRF, EDN1, MT2A, CLDN5 CXCL2, CYR61, RAMP2, DUSP1, FOSB, COL1A2, GNG11, CD93, SPARC, KLF2 Negative: DES, CTSL, LY6H, TPM2, GREM1, ISLR, HSPB6, PLAT, KCNK3, SFRP1 ACTG2, CNN1, MFAP4, MYL9, SCRG1, DPT, TGFBI, CA2, PDGFRA, TAGLN LEFTY2, CPE, FGL2, FXYD6, PTGER1, SYNM, IGFBP5, AC008397.2, SELENOM, PODN PC_ 5 Positive: IGKC, IGHA1, IGLC2, JCHAIN, IGLC3, IGHG2, IGHM, IGHG1, IGHG3, MZB1 IGHA2, MUC5AC, AGR2, H2AFZ, IGHGP, MALAT1, DES, AD000090.1, PIM2, RRM2 PRSS2, KRT8, MMP1, TFPI2, PTGDS, CA9, EGFL7, PTGER1, TFF3, GPX2 Negative: FN1, MGP, SERPINA1, GP2, CTGF, IGFBP7, DEPP1, COMP, COL1A1, MUC6 APOE, PHGR1, LGALS4, LINC01133, RFLNA, PIGR, FCGBP, SPARC, ZFP36, TM4SF1 PSCA, GKN1, LTF, LYZ, COL6A3, IFI27, BPIFB1, CEACAM5, GKN2, PLAC8 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 11:11:54 UMAP embedding parameters a = 0.9922 b = 1.112 11:11:54 Read 2624 rows and found 10 numeric columns 11:11:54 Using Annoy for neighbor search, n_neighbors = 30 11:11:54 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 11:11:55 Writing NN index file to temp file /tmp/RtmpwHiUgY/file55f187eab79a9 11:11:55 Searching Annoy index using 1 thread, search_k = 3000 11:11:56 Annoy recall = 100% 11:11:57 Commencing smooth kNN distance calibration using 1 thread 11:11:58 Initializing from normalized Laplacian + noise 11:11:58 Commencing optimization for 500 epochs, with 107958 positive edges 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 11:12:10 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: 2624 Number of edges: 83846 Running Louvain algorithm... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.8159 Number of communities: 12 Elapsed time: 0 seconds [1] 3000 2624 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 5 5 7 8 8 10 10 11 13 12 14 15 15 15 16 15 18 18 21 19 16 [1] "13" $m_MUC6 [1] "MUC6" "LYZ" "TFF2" "MSMB" "PIGR" [6] "PGC" "OLFM4" "REG1A" "AC020656.1" "BPIFB1" [11] "SERPINA1" "TFF3" "GP2" "LIPF" "SPINK1" [16] "FAM3D" "GAST" "AQP5" "MUC1" "TCN1" [21] "LTF" "AC139749.1" "ZG16B" "CXCL17" "C6orf58" [26] "LCN2" "KCNN4" "GOLM1" "PDIA2" "SPDEF" [31] "KIAA1324" "REG3A" $m_RBM6 [1] "RBM6" "SPG7" "MIB2" "KRR1" "TCERG1" "NDFIP2" [7] "SCML1" "PHACTR4" "CDC73" "ADNP" "TRIM41" "INTS6" [13] "MIGA2" "SHC2" "LUC7L" "PACSIN3" "GTPBP3" "STK3" [19] "EP400" "RTKN" "UTP14C" "CDK10" "ELF2" "C19orf48" [25] "SGSM2" "ZNF316" "ANKZF1" "ZFP91" "SLC26A6" "ZBTB3" [31] "ZNF646" "HELZ" "EAF1" "CAPRIN2" "ZNF205" "ERCC4" $m_KRT19 [1] "KRT19" "MUC5AC" "AKR1B10" "KRT8" "S100P" [6] "TFF1" "GKN1" "MUCL3" "GKN2" "GPX2" [11] "KRT18" "LGALS4" "AGR2" "PSCA" "ANXA10" [16] "TSPAN8" "CTSE" "FCGBP" "PHGR1" "JPT1" [21] "C19orf33" "CLDN18" "NQO1" "CAPN8" "TSPAN1" [26] "IFI27" "CYSTM1" "S100A14" "SULT1C2" "TMEM54" [31] "RFLNA" "IL1R2" "SDCBP2" "CD24" "ALDH3A1" [36] "LINC01133" "GALE" "AKR1C3" "OCIAD2" "LGALS3" [41] "FXYD3" "AKR7A3" "EPS8L1" "S100A11" "MAL2" [46] "SMIM22" "VILL" "EZR" "CEACAM5" "AGR3" [51] "H2AFZ" "LAMB3" "PERP" "VSIG1" "VSIG2" [56] "PLAC8" "TRNP1" "HPGD" "S100A10" "AC008397.1" [61] "S100A16" "TACSTD2" "ISG20" "SLPI" "NKX6-2" [66] "CYP2S1" "BCAS1" "DDX60" "KRT7" "MISP" [71] "ITGB4" "MYEOV" "EFHD2" "AADAC" "STARD10" [76] "MGST1" "C15orf48" "ELF3" "KLF4" "SMIM6" $m_IGKC [1] "IGKC" "IGLC2" "IGHA1" "IGLC3" "JCHAIN" "IGHG2" "IGHG1" "IGHG3" [9] "IGHM" "MZB1" "IGHA2" "NCAPH2" "IGHGP" "CDCA4" "SYMPK" $m_LY6H [1] "LY6H" "PLAT" "CTSL" "ISLR" "DPT" [6] "SFRP1" "PENK" "KCNK3" "HSPB6" "FXYD6" [11] "PDGFRA" "GPX3" "C7" "FGL2" "CPE" [16] "LEFTY2" "A2M" "MFAP4" "SCRG1" "TTC1" [21] "SPON1" "IGFBP5" "AC008397.2" "LY6E" "IFI6" [26] "PSD" "SYNM" "HAPLN1" "GPBAR1" "ANO1" [31] "PODN" "PDE1B" "CXCL14" "PTP4A3" "RBP1" [36] "ADAMTSL2" "PLAGL1" "NES" "CD14" "TIMP1" [41] "C1QTNF2" "CA2" "OBSCN" "CDC42EP2" $m_ATPAF2 [1] "ATPAF2" "ATAD2B" "ECSIT" "TPSAB1" "UBA6" "PITPNM2" "ANKRD11" [8] "LRSAM1" "MAF" "DGKH" "SOS2" "RECQL5" "PCNX3" "SLC27A1" [15] "ASXL2" "GIGYF1" "TMEM116" "ATP7A" $m_HLA_DRA [1] "HLA-DRA" "CD74" "HLA-DRB1" "HLA-DQA1" "HLA-DPB1" "CD52" [7] "HLA-DQB1" "HLA-DPA1" "C1QB" "CXCR4" "APOC1" "TYROBP" [13] "C1QA" "C1QC" "HMOX1" "APOE" "TRBC2" "LAPTM5" [19] "HLA-DRB5" "CCL5" "LCP1" "CORO1A" "LTB" "PTPRC" [25] "SOD2" "SRGN" "CCL4" "LGALS2" "FYB1" "GNLY" [31] "RGS1" "MGP" "SLA" "CCL19" "NKG7" "TRBC1" [37] "CXCL10" "RGS10" "CCL4L2" "LCP2" "GZMA" "KLRB1" $m_VWF [1] "VWF" "AQP1" "PECAM1" "GNG11" "CLDN5" "COL4A1" [7] "RAMP2" "ACKR1" "SLCO2A1" "CDH5" "HYAL2" "CD93" [13] "RAMP3" "CRIP2" "EDN1" "EGFL7" "APLNR" "IGFBP7" [19] "EPAS1" "CAV1" "SERPINE1" "FBLN2" "SHANK3" "DEPP1" [25] "PTPRB" "KLF2" "ENG" "APOLD1" "COL4A2" "ROBO4" [31] "PLVAP" "NOTCH3" "ITGA5" "TM4SF1" "GJA4" "CXCL2" [37] "ADAMTS1" "JAG1" $m_AD000090.1 [1] "AD000090.1" "MALAT1" "EHBP1L1" "MBD3" "TCIRG1" [6] "COL27A1" "TYMP" "PGGHG" "NKTR" "NDUFV1" [11] "KAT2A" $m_ACADS [1] "ACADS" "HIST1H4C" "PNISR" "ANKRD26" "ARGLU1" "SPECC1L" [7] "ZFX" "NUP160" "INPPL1" "SUPT5H" "TAF4" "FAAP100" [13] "STK11" "NCOR1" "UACA" "ZNF358" "WDR27" "CABIN1" [19] "INTS11" "PARP10" "AKAP9" "ZNF654" "PCNT" "ADAM19" [25] "BCL7C" "GOLGA4" "DNAJC16" "ARMH3" "TENT4A" "NEPRO" [31] "UBN2" "EIF2B4" "CISD2" "PER3" "INTU" "BICRA" [37] "API5" "NEAT1" "GMPS" "SELENOO" $m_TAGLN [1] "TAGLN" "DES" "MYL9" "ACTG2" "TPM2" "GREM1" [7] "ACTA2" "CNN1" "MYH11" "FLNA" "PPP1R14A" "CSRP1" [13] "PTGER1" "TPM1" "AEBP1" "HSPB1" "SYNPO2" "CRYAB" [19] "MYLK" "ELN" "PITX1" "CALD1" "MYL6" "ACTC1" [25] "LGALS1" "LMOD1" "PDLIM3" "WFDC1" "FLNC" "FHL1" $m_HBB [1] "HBB" "ENAH" "ADIRF" "HBA2" "PIEZO1" "RBM38" [7] "THBS1" "DAG1" "EFEMP1" "TUBB6" "GADD45B" "NUBP2" [13] "VCL" "MT2A" "UTP3" "METRNL" "TNFRSF12A" "ADCK5" [19] "SPP1" "TRIL" "BABAM1" "ESS2" "ZNF22" "MAP3K7CL" [25] "WDR13" "TGFBR1" "ZBTB17" "PPP1R12A" "HBA1" "RNF217" [31] "IGFBP6" "PARD3B" "CCNG2" "UQCRC1" "TMEM268" "TPRA1" [37] "MPHOSPH8" "INHBA" "OTUD3" $m_COL1A1 [1] "COL1A1" "COL1A2" "FOSB" "COL6A3" "LUM" [6] "COL3A1" "BGN" "SFRP2" "COMP" "FOS" [11] "CCDC80" "COL5A1" "PTGDS" "FN1" "COL8A1" [16] "CFD" "CCL11" "FBLN1" "THBS2" "TNXB" [21] "PI16" "SPARC" "ADAMTS2" "CLEC11A" "CTHRC1" [26] "MEG3" "ADH1B" "NBL1" "POSTN" "CCL21" [31] "THBS4" "EGR1" "JUN" "AC020916.1" "SVEP1" [36] "CTGF" "COL12A1" "TIMP3" "COL14A1" "MFGE8" [41] "MRC2" "SULF1" "ENC1" "MFAP2" "IER2" [46] "DKK3" "CYR61" "TPSB2" "SMG5" "VMP1" [51] "TMEM119" "GAS1" "PLAC9" 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 Calculating cluster 9 Calculating cluster 10 Calculating cluster 11 Warning message: CombinePlots is being deprecated. Plots should now be combined using the patchwork system. Calculating cluster m_MUC6 Calculating cluster m_KRT19 Calculating cluster m_LY6H Calculating cluster m_HLA_DRA Calculating cluster m_VWF Calculating cluster m_AD000090.1 Calculating cluster m_TAGLN Calculating cluster m_COL1A1 Warning message: CombinePlots is being deprecated. Plots should now be combined using the patchwork system. null device 1