GeorgescuC
commented
1 year ago Hi @dbswls0322 ,
Based on your comment, I assume you were trying to reduce the number of subclusters. In that case, you should lower the leiden_resolution parameter rather than increase it, with the default value being 0.05. You get this error when using 0.9 because every single cell is assigned a unique subcluster with such a high resolution, which means all leaves of the dendrogram are parallel and there is no root.
For more information about how to check the subclustering quality, you can also check the video tutorial that is now available.
Regards, Christophe.
dbswls0322
Hi, guys I got error in step 15 when calculating subcluster.
Originally, I didn't set value for leiden_resolution. But when I let it as default, the number of subclusters was more than 1200.
So I really want to solve this problem. Please help me.
This is my code. infercnv_obj2 = infercnv::run(nfercnv_obj2 , cutoff=0.1, # cutoff=1 works well for Smart-seq2, and cutoff=0.1 works well for 10x Genomics out_dir="./subcluster", cluster_by_groups=F, denoise=TRUE, HMM=TRUE, leiden_resolution=0.9 )
This is my error
INFO [2023-06-15 15:45:02] define_signif_tumorsubclusters(), tumor: Hepatocyte Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| Centering and scaling data matrix |=====================================================================| 100% PC 1 Positive: POLR2A, CHRNB1, EIF4A1, CD68, TMEM256, MPDU1, GPS2, SHBG, EIF5A, CLDN7 SAT2, ELP5, CTDNEP1, TP53, GABARAP, KDM6B, PHF23, NAA38, DVL2, ACADVL TRAPPC1, ASGR1, PER1, ASGR2, SLC16A11, VAMP2, C17orf49, RNASEK, XAF1, SLC13A5 Negative: USP38, SMARCA5, ZNF330, TBC1D9, ELMOD2, CLGN, HSPA4L, NUDT6, SPRY1, SCOC LARP1B, KIAA1109, PGRMC2, BBS7, MGST2, JADE1, SETD7, EXOSC9, RAB33B, ELF2 NDUFC1, NAA15, ANXA5, MAD2L1, C4orf3, USP53, SEC24D, METTL14, SNHG8, CAMK2D PC 2 Positive: C1orf43, UBAP2L, HAX1, TPM3, IL6R, RPS27, UBE2Q1, RAB13, SMU1, B4GALT1 JTB, ADAR, SPINK4, STXBP2, PET100, CREB3L4, TRAPPC5, XAB2, MAP2K7, BAG1 PMVK, TGFBR3L, CAMSAP3, CHMP5, SNAPC2, SLC39A1, PNPLA6, PBXIP1, TIMM44, NFX1 Negative: AUTS2, POM121, TYW1, NSUN5, OOEP, B3GAT2, MTO1, SMAP1, RARS2, KHDC1L RNGTT, ORC3, EEF1A1, SLC17A5, SLC35A1, CD109, AKIRIN2, COX7A2, SBDS, SMIM8 PNRC1, ZNF292, SDHAF4, TMEM30A, BAZ1B, TMEM248, SYNCRIP, SENP6, PM20D2, LMBRD1 PC 3 Positive: SLC16A7, USP15, CTDSP2, TSFM, MON2, METTL1, TMEM5, CDK4, SRGAP1, TSPAN31 C12orf66, OS9, XPOT, TBK1, PIP4K2C, RASSF3, SH3BGRL2, DCTN2, BCKDHB, HMGN3 GNS, FAM46A, IBTK, PHIP, UBE3D, TPBG, PGM3, MYO6, ME1, SENP6 Negative: RSBN1L, APTR, TMEM60, GNAI1, PTPN12, CD36, HGF, DMTF1, TMEM243, FGL2 TP53TG1, CROT, DTX2, ABCB4, YWHAG, ABCB1, HSPB1, SLC25A40, MDH2, STYXL1 DBF4, TMEM120A, POR, SRI, RHBDD2, CCL26, STEAP1, HIP1, POM121C, STEAP2 PC 4 Positive: FAHD2B, ACTR1B, COX5B, ANKRD39, LMAN2L, TMEM131, KANSL3, COA5, ARID5A, UNC50 SNRNP200, MGAT4A, CIAO1, TMEM127, STARD7, LIPT1, DUSP2, MITD1, GPAT2, MRPL30 ANKRD36C, TXNDC9, EIF5B, FAHD2A, REV1, ZNF514, PDCL3, RPL31, MRPS5, CNOT11 Negative: UBQLN4, LAMTOR2, SSR2, MEX3A, ARHGEF2, KIAA0907, LMNA, RIT1, SLC25A44, EED GON4L, PICALM, CREBZF, PRSS23, TMEM126A, PMF1, TMEM126B, TMEM135, SMG5, DAP3 CCDC90B, CTSC, PCF11, GLMP, RAB30-AS1, CCT3, CHORDC1, PRCP, YY1AP1, SLC36A4 PC 5 Positive: UBE2Q2, IMP3, FBXO22, ETFA, SNUPN, SCAPER, SIN3A, RCN2, MAN2C1, TSPAN3 HMG20A, NEIL1, TBC1D2B, COMMD4, CIB2, C15orf39, IDH3A, DNAJA4, WDR61, CRABP1 IREB2, PSMA4, MORF4L1, CTSH, TMED3, MTHFS, ST20, BCL2A1, ZFAND6, FAH Negative: MMP1, MMP7, MMP12, DCUN1D5, TMEM123, BIRC2, BIRC3, CASP4, YAP1, CASP1 CARD16, CCDC82, MSANTD4, MTMR2, KBTBD3, CEP57, AASDHPPT, FAM76B, CWF19L2, SESN3 CUL5, SRSF8, ACAT1, CWC15, ANKRD49, PANX1, MED17, C11orf54, TAF1D, SMCO4 Computing nearest neighbor graph Computing SNN Error in UseMethod("is.rooted") : no applicable method for 'is.rooted' applied to an object of class "NULL"