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] "BRCAHs0" 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 17252 by 2384 Model formula is y ~ log_umi Get Negative Binomial regression parameters per gene Using 2000 genes, 2384 cells | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% Found 48 outliers - those will be ignored in fitting/regularization step Second step: Get residuals using fitted parameters for 17252 genes | | | 0% | |== | 3% | |==== | 6% | |====== | 9% | |======== | 11% | |========== | 14% | |============ | 17% | |============== | 20% | |================ | 23% | |================== | 26% | |==================== | 29% | |====================== | 31% | |======================== | 34% | |========================== | 37% | |============================ | 40% | 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|================================================================ | 91% | |================================================================== | 94% | |==================================================================== | 97% | |======================================================================| 100% Computing corrected count matrix for 17252 genes | | | 0% | |== | 3% | |==== | 6% | |====== | 9% | |======== | 11% | |========== | 14% | |============ | 17% | |============== | 20% | |================ | 23% | |================== | 26% | |==================== | 29% | |====================== | 31% | |======================== | 34% | |========================== | 37% | |============================ | 40% | |============================== | 43% | |================================ | 46% | |================================== | 49% | |==================================== | 51% | |====================================== | 54% | |======================================== | 57% | 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gene attributes Wall clock passed: Time difference of 1.412247 mins Determine variable features Set 3000 variable features Place corrected count matrix in counts slot Centering data matrix | | | 0% | |=== | 4% | |====== | 8% | |========= | 12% | |============ | 17% | |=============== | 21% | |================== | 25% | |==================== | 29% | |======================= | 33% | |========================== | 38% | |============================= | 42% | |================================ | 46% | |=================================== | 50% | |====================================== | 54% | |========================================= | 58% | |============================================ | 62% | |=============================================== | 67% | |================================================== | 71% | |==================================================== | 75% | |======================================================= | 79% | |========================================================== | 83% | |============================================================= | 88% | |================================================================ | 92% | |=================================================================== | 96% | |======================================================================| 100% Set default assay to SCT There were 50 or more warnings (use warnings() to see the first 50) PC_ 1 Positive: SGK3, COX6C, GRB14, DHRS2, UGDH, YWHAZ, MGP, SCD, SLC39A6, CPB1 MGST1, UQCRB, TFPI2, MAL2, CD24, PDCD4, POLR2K, SUB1, SPINT2, KRT15 ELOC, TMEM64, ENY2, PFDN4, NDUFB9, PPDPF, GPRC5A, RAD21, TFF1, XBP1 Negative: CCL19, TRBC2, C3, PTGDS, CD52, CCL21, HLA-DRA, TXNIP, TRAC, HLA-DPB1 TRBC1, CD74, IL32, HLA-DPA1, CXCR4, ACKR1, COL1A1, S100A4, HLA-DRB1, CORO1A IFITM2, HLA-DQA1, IGFBP7, LSP1, LIMD2, HLA-DQB1, VWF, IL7R, VIM, COL1A2 PC_ 2 Positive: TRBC2, TRAC, CD52, CXCR4, TRBC1, HLA-DRA, PTGDS, CCL19, IL7R, GZMB TXNIP, B2M, TMSB4X, GPR183, CD3E, HLA-DPA1, HLA-DQA1, IL2RG, CD3D, CCR7 RAC2, MMP9, BIRC3, ARHGDIB, LIMD2, LCP1, CORO1A, CD74, CD247, CD53 Negative: COL1A1, COL1A2, TAGLN, ADIRF, SPARC, COL3A1, CTGF, MYL9, ACTA2, FN1 AEBP1, POSTN, BGN, COL6A2, DCN, IGFBP7, SFRP2, ID3, AQP1, TIMP3 NDUFA4L2, KRT17, IFI27, IGFBP4, HTRA3, TNXB, KRT14, COL18A1, ELN, CST1 PC_ 3 Positive: VWF, ACKR1, SPARCL1, TSPAN7, PECAM1, COL15A1, EPAS1, IGFBP7, GNG11, SELP AQP1, ACTA2, A2M, PLVAP, CSRP2, CD93, B2M, YWHAZ, RAMP3, COL4A1 TM4SF1, IL33, STOM, SGK3, EGFL7, S1PR1, ADAMTS1, VIM, IFITM2, PDLIM1 Negative: IGHA1, IGLC2, IGLC3, IGHG1, IGHM, IGHG3, IGHG4, IGHG2, JCHAIN, IGKC MZB1, IGHA2, CTSD, C1QA, COL1A1, APOC1, KRT8, H2AFJ, FTL, ISG15 KRT18, CST1, RAMP1, TFF3, ELOB, TFF1, C1QB, MDK, KRT19, BLVRB PC_ 4 Positive: ACKR1, CCL21, CCL19, VWF, IGLC3, ADIRF, TFF1, PTGDS, TFF3, H2AFJ SNCG, EGFL7, KRT18, ISG15, KRT8, ENG, AD000090.1, CLDN5, BLVRB, CALML5 ELOB, GPX3, KRT19, MDK, IGHG2, RAMP3, SMIM22, RAMP1, SELENOM, CYC1 Negative: COL1A1, COL3A1, COL1A2, POSTN, FN1, SPARC, LYZ, CST1, HLA-DRA, LUM TMSB4X, COL6A3, COL6A1, HLA-DQA1, B2M, HLA-DPA1, COL5A1, IGHG3, THBS4, GPNMB NPC2, COL5A2, TIMP1, CXCL9, JCHAIN, SFRP2, MXRA5, HTRA3, MGP, THBS2 PC_ 5 Positive: KRT17, KRT14, KRT6B, S100A2, KRT5, CHI3L1, MMP7, TNC, IGHG1, SAA1 APOC1, A2M, MYLK, TACSTD2, IGLC3, NPC2, LYZ, COL17A1, PTN, RGS5 CALML3, IGHA1, IGHG4, ITGB6, IGLC2, CDH3, TPSAB1, CXCL10, SFN, SGK1 Negative: COL1A1, C3, COL1A2, COL3A1, DCN, LUM, SFRP2, CCDC80, COL6A3, FBLN1 POSTN, GRB14, SGK3, TNXB, MMP2, COL6A2, COL6A1, THBS2, SFRP4, UGDH CTGF, LRP1, DHRS2, VCAN, FBLN2, MFAP4, BGN, AEBP1, TMEM119, C1S 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 10:11:09 UMAP embedding parameters a = 0.9922 b = 1.112 10:11:09 Read 2384 rows and found 10 numeric columns 10:11:09 Using Annoy for neighbor search, n_neighbors = 30 10:11:09 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 10:11:10 Writing NN index file to temp file /tmp/RtmpeuKHfQ/file296b037d2add1 10:11:10 Searching Annoy index using 1 thread, search_k = 3000 10:11:11 Annoy recall = 100% 10:11:12 Commencing smooth kNN distance calibration using 1 thread 10:11:15 Initializing from normalized Laplacian + noise 10:11:15 Commencing optimization for 500 epochs, with 97342 positive edges 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 10:11:27 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: 2384 Number of edges: 77620 Running Louvain algorithm... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.7694 Number of communities: 10 Elapsed time: 0 seconds [1] 3000 2384 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 5 5 7 7 8 9 11 11 11 11 14 15 14 17 18 18 18 21 20 23 23 [1] "11" $m_SNCG [1] "SNCG" "RAMP1" "TFF3" "AD000090.1" "BLVRB" [6] "ELOB" $m_ACKR1 [1] "ACKR1" "VWF" "PECAM1" "SPARCL1" "RAMP3" "AQP1" "TSPAN7" [8] "COL15A1" "SELP" "FABP4" "PLVAP" "EGFL7" "TGFBR2" "ENG" [15] "IL33" "CAVIN2" "SPNS2" "ECSCR" "CXorf36" "IFITM2" "CD93" [22] "SPRY1" "EPAS1" "CSRP2" "PRCP" "IGFBP7" "LIFR" "PDLIM1" [29] "PDK4" "GNG11" "JAM2" "MMRN2" $m_TNXB [1] "TNXB" "PLAC9" "ISG15" "CFD" "PI16" "DEPP1" "GGT5" "CLDN5" [9] "FXYD1" "ADAM33" "VAMP5" "ADIRF" "MEG3" "SOD3" "LRRC32" "IGFBP4" [17] "CAVIN1" $m_COL1A1 [1] "COL1A1" "COL1A2" "COL3A1" "POSTN" "LUM" "SFRP2" [7] "COL6A3" "DCN" "CCDC80" "COL6A1" "CTGF" "FN1" [13] "BGN" "THBS2" "VCAN" "COL5A1" "COL6A2" "SFRP4" [19] "HTRA3" "THBS4" "COL5A2" "FBLN1" "MMP2" "MXRA5" [25] "EFEMP1" "SPARC" "C3" "CST1" "TIMP3" "LRP1" [31] "TIMP1" "ELN" "SPON2" "CILP" "COL12A1" "FSTL1" [37] "FBLN2" "TMEM119" "AEBP1" "CTHRC1" "CDH11" "CTSK" [43] "MMP11" "MFAP5" "FBN1" "PCOLCE" "SULF1" "MFAP4" [49] "CXCL14" "COL14A1" "ISLR" "COL16A1" "PODN" "C1S" [55] "COMP" "SERPINE2" "P3H3" "MXRA8" "PTGIS" "IGFBP6" [61] "COL8A1" "LOX" "SERPINF1" "NBL1" "THY1" "ASPN" [67] "DPT" "PRELP" "CD248" "MFAP2" "MRC2" "CERCAM" $m_RGS5 [1] "RGS5" "COL4A1" "PODXL" "ACTA2" "PLPP1" "MCAM" [7] "CSPG4" "COL4A2" "NDUFA4L2" "GJA4" "FLT1" "A2M" [13] "TMEM204" $m_IGHG1 [1] "IGHG1" "IGHA1" "IGHG4" "IGHG3" "IGHM" "IGLC2" "JCHAIN" [8] "IGLC3" "IGHG2" "IGHA2" "MZB1" "IGKC" "IGHGP" "FKBP11" [15] "DERL3" "TPSB2" "TPSAB1" "IGLL5" "IGLC6" "IGLV3-1" "IGLC7" [22] "CPNE5" "CTSG" "FCRL5" $m_SGK3 [1] "SGK3" "CPB1" "GRB14" "COX6C" "DHRS2" "UGDH" [7] "YWHAZ" "SCD" "SLC39A6" "MGST1" "TFPI2" "UQCRB" [13] "MAL2" "CD24" "MGP" "POLR2K" "PDCD4" "SUB1" [19] "TMEM64" "ELOC" "GPRC5A" "ENY2" "SPINT2" "S100A7" [25] "RAD21" "PFDN4" "XBP1" "RAB2A" "SCUBE2" "PLA2G16" [31] "WWP1" "SMS" "CALM2" "COX6A1" "TBCA" "TPD52" [37] "ATP9A" "MPC2" "PABPC1" "GLUL" "TBC1D9" "SMIM14" [43] "NDUFB9" "KRT15" "IFIT1" "SDC4" "CDH1" "ARFGEF1" [49] "LYPLA1" "CA12" "PARD6B" "UBE2V2" "NUCB2" "DSTN" [55] "AGR2" "PPDPF" "GATA3" "ESRP1" "ACADSB" "TFF1" [61] "PPP1R3C" "SFMBT1" "HSPB8" "TPD52L1" "ARMT1" "UBE2C" [67] "PKIB" "NFKBIZ" "STC2" "CD9" "RDH10" "PDZK1" [73] "TNFSF10" "PABPC1L" "SLC9A3R1" "TRPA1" "TMPRSS4" "C15orf48" [79] "SERPINI1" "HMGCS2" "BEX1" "ABHD2" "PRSS1" "MAGED2" [85] "IFI6" "PIP" "RHPN1" "S100A14" "S100A9" $m_KRT14 [1] "KRT14" "KRT5" "KRT17" "MMP7" "KRT81" "KRT6B" [7] "S100A2" "TNC" "LTF" "CRYAB" "RARRES1" "PTN" [13] "TACSTD2" "FDCSP" "KLK5" "ACTG2" "SLPI" "CALML3" [19] "MT1X" "SAA2" "TRIM29" "KRT23" "KLK7" "MT2A" [25] "SPP1" "SFN" "GABRP" "ITGB6" "GPX2" "KRT16" [31] "CDH3" "MYLK" "LCN2" "COL17A1" "MT1E" "NPC2" [37] "S100A16" "ITGB4" "CHI3L1" "PDZK1IP1" "FOS" "SAA1" [43] "KRT7" "SGK1" "ANPEP" "CST6" "KLK10" "FOSB" [49] "NGFR" "JUN" "ITGA3" "EGR1" "MT1M" "STAC2" [55] "PDLIM4" "LTBP2" "KLHDC7B" "THBS1" "GPC1" $m_PTGDS [1] "PTGDS" "CXCR4" "GZMB" "RASGRP2" "MS4A1" "CCL21" "GPR183" [8] "TXNIP" $m_HLA_DRA [1] "HLA-DRA" "CCL22" "HLA-DPA1" "TMSB4X" "TRAC" "CXCL9" [7] "HLA-DQA1" "CCL17" "IL32" "FSCN1" "HLA-DPB1" "TRBC2" [13] "TRBC1" "HLA-DQB1" "LGALS2" "LCP1" "CD52" "B2M" [19] "MMP9" "CCL5" "EBI3" "SRGN" "LAMP3" "ARHGDIB" [25] "LSP1" "S100A4" "CD3D" "TNFAIP3" "IL2RG" "HLA-DRB1" [31] "RASSF4" "CD1E" "CD74" "BIRC3" "CXCL13" "BATF" [37] "PTPRC" "TNFRSF4" "COTL1" "CD5" "CD3E" "CD2" [43] "CLEC10A" "SPOCK2" "GMFG" "PPP1R18" $m_APOC1 [1] "APOC1" "LYZ" "C1QB" "C1QC" "APOE" [6] "GPNMB" "CCL18" "C1QA" "TYROBP" "LGMN" [11] "NR1H3" "CD68" "CTSS" "FCER1G" "IFI30" [16] "CYP27A1" "CAPG" "CD14" "FTL" "LILRB4" [21] "TREM2" "SDS" "HMOX1" "CSF1R" "GCHFR" [26] "CTSC" "SLC15A3" "MS4A6A" "PLA2G2D" "AIF1" [31] "HLA-DRB5" "CCL4L2" "AC020656.1" "ITGB2" "CHCHD6" [36] "SIGLEC1" "C2" "LAPTM5" 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 Warning message: CombinePlots is being deprecated. Plots should now be combined using the patchwork system. Calculating cluster m_SNCG Calculating cluster m_ACKR1 Calculating cluster m_TNXB Calculating cluster m_COL1A1 Calculating cluster m_RGS5 Calculating cluster m_IGHG1 Calculating cluster m_SGK3 Calculating cluster m_KRT14 Calculating cluster m_PTGDS Calculating cluster m_HLA_DRA Warning message: CombinePlots is being deprecated. Plots should now be combined using the patchwork system. null device 1