Convert a Seurat Object to a Monocle Cell Data Set
convert_seu_to_cds(seu, resolution = 1, min_expression = 0.05)processed_seu <- clustering_workflow(human_gene_transcript_seu)
#> Centering and scaling data matrix
#> Centering and scaling data matrix
#> PC_ 1
#> Positive: CNGB1, RBP3, GUCA1A, IMPG1, GUCA1B, ROM1, PDE6B, GNAT1, LINC02528, NR2E3
#> GNGT1, GUCA1C, MYL4, ARR3, SPINK4, AC023905.1, SAG, GNB1, ISOC1, VTN
#> SLC39A5, AC112206.2, CCKBR, CNGB3, AP000997.1, SLC40A1, MT1X, FABP12, PDE6A, AC118942.1
#> Negative: AC011270.2, IFITM3, IFITM2, CLU, SFRP2, DKK3, CCND1, SERPING1, CA14, VIM
#> HES1, IFITM1, MDK, BCHE, NKAIN4, CRABP1, PAX6, CYR61, LAMP5, RAB31
#> TRH, MYB, CYP26A1, FBLN1, PRSS35, TMEM98, PON2, CDH11, ASCL1, OAF
#> PC_ 2
#> Positive: GNAT1, GNGT1, GNB1, ROM1, NR2E3, SAG, CNGB1, PDE6A, AC002076.2, YBX3
#> RHO, LINC02115, CLUL1, PDE6B, HTRA1, PPEF2, WAPL, AP000997.1, CCKBR, DUSP1
#> IRX6, GABRR3, CTSV, MRLN, PDLIM1, IMPG1, SLC24A1, ID1, RBP3, NT5E
#> Negative: MIR7-3HG, RBP4, ISL2, THRB, DCT, DLL3, ARR3, APOE, SPON2, NNAT
#> DCX, SYT4, SSTR2, TMSB4X, STMN2, TMSB4XP8, ANXA2, C15orf59-AS1, FILIP1L, SLC1A6
#> AL359757.1, DPP10, CLDN5, MUSTN1, RASD1, SCD, KLHL35, AC023905.1, GRIA3, FAM19A3
#> PC_ 3
#> Positive: WIF1, ANGPTL1, DACT2, CFI, C1orf61, OAF, PYGL, CP, PLP1, F3
#> FKBP10, DKK3, TOX3, CREB5, TRPM3, RRH, HLA-E, SERPING1, CD44, COL9A3
#> LAMP5, RBP1, TRH, GDPD2, WWTR1, FRZB, MIR100HG, EFEMP1, SPTLC3, SELENOP
#> Negative: AURKB, DLGAP5, PBK, BIRC5, TPX2, CCNB2, RRM2, CDC20, CCNA2, KIF20A
#> KIF23, PIMREG, TROAP, BUB1, SPC25, HJURP, NUF2, NEIL3, ANLN, POC1A
#> CDK1, MELK, CDCA8, OIP5, KIF2C, GTSE1, ZWINT, PRC1, PLK1, CENPM
#> PC_ 4
#> Positive: GUCA1C, AC023905.1, CNGB3, MYL4, GUCA1B, ARR3, GSN, GUCA1A, AC112206.2, AC103740.1
#> RAB41, TTR, TDRG1, LINC02528, SLC39A5, AC092966.1, MT1F, GLYATL1, GPX3, OPN1MW
#> OPN1MW2, FAIM, OPN1LW, OPN1MW3, IGFBP7, C9orf135, CXCL14, IMPG1, TRPM3, DMKN
#> Negative: TMSB4XP8, TMSB4X, STMN2, RBP1, SSTR2, DCX, NNAT, MRLN, SYT4, DCT
#> H2AFY2, TMSB15A, DLL3, RASD1, IRX6, NR2E3, GALP, GSG1, AC010247.2, SH3BGRL
#> CRABP1, CPLX3, SNCG, TMEM176A, TMEM176B, SCHIP1, SPON2, DPP10, ISOC1, FILIP1L
#> PC_ 5
#> Positive: VAT1L, PIP5K1B, HTR2C, GMNC, TPD52L1, CXCL14, DMKN, AL590094.1, CPS1, S100A11
#> GMPR, HSD17B2, ANXA1, LGALS1, ALDH1A1, BLNK, ZIC4-AS1, TM4SF1, TYR, AC073349.1
#> C21orf62, AL049777.1, CA12, ADH1C, ZIC4, AIFM3, MGST2, RHOJ, TRPM3, GPNMB
#> Negative: WIF1, LAMP5, GUCA1C, SFRP2, AC023905.1, ANGPTL1, ARR3, CNGB3, TRH, AC011270.2
#> PRSS35, MYL4, DACT2, GUCA1B, BCHE, LINC01658, WWTR1, RAB41, COL2A1, VSX2
#> CRYM, CDH11, MLLT3, TTYH1, GUCA1A, AC112206.2, AC103740.1, EFNA1, CREB5, HES5
#> Warning: The following arguments are not used: check_duplicates
#> 13:34:16 UMAP embedding parameters a = 0.9922 b = 1.112
#> Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
#> Also defined by 'spam'
#> 13:34:16 Read 883 rows and found 30 numeric columns
#> 13:34:16 Using Annoy for neighbor search, n_neighbors = 30
#> Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
#> Also defined by 'spam'
#> 13:34:16 Building Annoy index with metric = cosine, n_trees = 50
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#> |
#> 13:34:17 Writing NN index file to temp file /tmp/RtmpLoWyKl/file32063234d4a409
#> 13:34:17 Searching Annoy index using 1 thread, search_k = 3000
#> 13:34:17 Annoy recall = 100%
#> 13:34:17 Commencing smooth kNN distance calibration using 1 thread
#> with target n_neighbors = 30
#> 13:34:18 Initializing from normalized Laplacian + noise (using RSpectra)
#> 13:34:18 Commencing optimization for 500 epochs, with 35966 positive edges
#> 13:34:19 Optimization finished
#> [13:34:19] Clustering Cells...
#> Computing nearest neighbor graph
#> Computing SNN
#> clustering at 0.2 resolution
#> Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
#>
#> Number of nodes: 883
#> Number of edges: 37588
#>
#> Running Louvain algorithm...
#> Maximum modularity in 10 random starts: 0.8961
#> Number of communities: 3
#> Elapsed time: 0 seconds
#> clustering at 0.4 resolution
#> Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
#>
#> Number of nodes: 883
#> Number of edges: 37588
#>
#> Running Louvain algorithm...
#> Maximum modularity in 10 random starts: 0.8291
#> Number of communities: 4
#> Elapsed time: 0 seconds
#> clustering at 0.6 resolution
#> Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
#>
#> Number of nodes: 883
#> Number of edges: 37588
#>
#> Running Louvain algorithm...
#> Maximum modularity in 10 random starts: 0.7898
#> Number of communities: 6
#> Elapsed time: 0 seconds
#> clustering at 0.8 resolution
#> Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
#>
#> Number of nodes: 883
#> Number of edges: 37588
#>
#> Running Louvain algorithm...
#> Maximum modularity in 10 random starts: 0.7542
#> Number of communities: 6
#> Elapsed time: 0 seconds
#> clustering at 1 resolution
#> Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
#>
#> Number of nodes: 883
#> Number of edges: 37588
#>
#> Running Louvain algorithm...
#> Maximum modularity in 10 random starts: 0.7208
#> Number of communities: 7
#> Elapsed time: 0 seconds
#> clustering at 1.2 resolution
#> Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
#>
#> Number of nodes: 883
#> Number of edges: 37588
#>
#> Running Louvain algorithm...
#> Maximum modularity in 10 random starts: 0.6892
#> Number of communities: 10
#> Elapsed time: 0 seconds
#> clustering at 1.4 resolution
#> Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
#>
#> Number of nodes: 883
#> Number of edges: 37588
#>
#> Running Louvain algorithm...
#> Maximum modularity in 10 random starts: 0.6613
#> Number of communities: 11
#> Elapsed time: 0 seconds
#> clustering at 1.6 resolution
#> Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
#>
#> Number of nodes: 883
#> Number of edges: 37588
#>
#> Running Louvain algorithm...
#> Maximum modularity in 10 random starts: 0.6345
#> Number of communities: 11
#> Elapsed time: 0 seconds
#> clustering at 1.8 resolution
#> Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
#>
#> Number of nodes: 883
#> Number of edges: 37588
#>
#> Running Louvain algorithm...
#> Maximum modularity in 10 random starts: 0.6079
#> Number of communities: 11
#> Elapsed time: 0 seconds
#> clustering at 2 resolution
#> Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
#>
#> Number of nodes: 883
#> Number of edges: 37588
#>
#> Running Louvain algorithm...
#> Maximum modularity in 10 random starts: 0.5815
#> Number of communities: 11
#> Elapsed time: 0 seconds
#> stashing presto markers for gene_snn_res.0.2
#> stashing presto markers for gene_snn_res.0.4
#> stashing presto markers for gene_snn_res.0.6
#> stashing presto markers for gene_snn_res.0.8
#> stashing presto markers for gene_snn_res.1
#> stashing presto markers for gene_snn_res.1.2
#> stashing presto markers for gene_snn_res.1.4
#> stashing presto markers for gene_snn_res.1.6
#> stashing presto markers for gene_snn_res.1.8
#> stashing presto markers for gene_snn_res.2
#> Warning: The following features are not present in the object: MCM5, PCNA, FEN1, MCM2, RRM1, UNG, GINS2, MCM6, CDCA7, PRIM1, UHRF1, MLF1IP, RFC2, RPA2, NASP, GMNN, WDR76, SLBP, UBR7, POLD3, MSH2, ATAD2, EXO1, TIPIN, DSCC1, BLM, CASP8AP2, CLSPN, POLA1, CHAF1B, BRIP1, E2F8, not searching for symbol synonyms
#> Warning: The following features are not present in the object: TMPO, CENPF, FAM64A, CKAP2, KIF11, ANP32E, TUBB4B, KIF20B, CDCA3, HN1, TTK, RANGAP1, NCAPD2, CDCA2, ECT2, HMMR, PSRC1, LBR, CKAP5, CTCF, G2E3, CBX5, not searching for symbol synonyms
#> [13:34:22] Logging Technical Details...
cds <- convert_seu_to_cds(processed_seu)
#> [1] 1
#> No preprocess_method specified, using preprocess_method = 'PCA'
#> Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
#> Also defined by 'spam'
#> Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
#> Also defined by 'spam'
#> Error in convert_seu_to_cds(processed_seu): no slot of name "preprocess_aux" for this object of class "cell_data_set"