我有一些数据CM
(下面),其中包括6个基因面板。面板中的一些基因重叠。我创建了一个维恩图,但我的主管希望数据以不同的格式呈现。他们希望面板之间的重叠由网络图表示。他们希望节点大小指的是基因面板的大小,而边缘指的是面板之间共享的基因,线的粗细对应于共有基因的数量)。
我完全不知所措,我甚至不知道如何处理数据,以适应像igraph的东西。
为了分解它,我可以计算每组中的基因数量:CM %>% group_by(Panel) %>% tally()
我也可以看看重叠:table(CM$Gene.Symbol, CM$Panel)
那我就卡住了...请对我宽容点,我是临床医生!
> dput(CM)
structure(list(Gene.Symbol = c("DES", "DSC2", "DSG2", "DSP",
"FLNC", "JUP", "LMNA", "PKP2", "PLN", "TMEM43", "ANK2", "CDH2",
"CAVIN4", "CTNNA3", "LDB3", "RBM20", "RYR2", "SCN5A", "TGFB3",
"TTN", "AARS2", "ABCC9", "ACAD9", "ACADVL", "ACTA1", "ACTC1",
"ACTN2", "AGK", "ALMS1", "ALPK3", "BAG3", "CACNA1C", "CDH2",
"COA5", "COA6", "COX10", "COX15", "CPT2", "CSRP3", "DES", "DMD",
"DNAJC19", "DOLK", "DSC2", "DSG2", "DSP", "EMD", "EPG5", "FHL1",
"FHOD3", "FKTN", "FLNC", "GAA", "GUSB", "HADHA", "HADHB", "HRAS",
"IDH2", "IDUA", "JPH2", "JUP", "KRAS", "LAMP2", "LMNA", "LZTR1",
"MAP2K1", "MAP2K2", "MLYCD", "MRAS", "MRPL44", "MUT", "MYBPC3",
"MYH6", "MYH7", "MYL2", "MYL3", "MYLK3", "MYPN", "NDUFA11", "NDUFA2",
"NDUFAF1", "NDUFB11", "NDUFS2", "NDUFS8", "NDUFV2", "NEXN", "NKX2-5",
"NONO", "NRAP", "NRAS", "PCCA", "PCCB", "PKP2", "PLD1", "PLN",
"PPA2", "PPCS", "PPP1CB", "PPP1R13L", "PRKAG2", "PTPN11", "RAF1",
"RBM20", "RIT1", "RYR2", "SCN5A", "SCO1", "SCO2", "SHOC2", "SLC22A5",
"SLC25A20", "SLC25A4", "SOS1", "SOS2", "SPEG", "TAZ", "TMEM43",
"TMEM70", "TNNC1", "TNNI3", "TNNI3K", "TNNT2", "TPM1", "TSFM",
"TTN", "TTR", "VCL", "AGL", "ANK2", "ARSB", "ATP5D", "ATPAF2",
"BRAF", "CBL", "COX14", "COX20", "COX6B1", "COX7B", "CRYAB",
"EYA4", "FAH", "FASTKD2", "FKRP", "FLII", "FNIP1", "FOXRED1",
"GATA6", "GLA", "GLB1", "GSN", "HCN4", "HFE", "HGSNAT", "IDS",
"LDB3", "LRPPRC", "MIB1", "MMACHC", "MT-TI", "NAA15", "NAGLU",
"NDUFA1", "NDUFA10", "NDUFA4", "NDUFAF2", "NDUFAF3", "NDUFAF4",
"NDUFAF5", "NDUFB3", "NDUFB8", "NDUFS1", "NDUFS3", "NDUFS4",
"NDUFS6", "NDUFS7", "NDUFV1", "NF1", "NUBPL", "PDLIM3", "PET100",
"PNPLA2", "RASA2", "RHBDF1", "RNF220", "RPL3L", "SDHA", "SDHAF1",
"SDHD", "SGCD", "SGSH", "SHMT2", "SLC30A5", "SPRED2", "SURF1",
"TMEM126B", "TOR1AIP1", "UQCC2", "ANKRD1", "APOPT1", "B3GAT3",
"BCS1L", "BTK", "COA7", "COX6A1", "CPS1", "CTF1", "CYC1", "DHCR7",
"DTNA", "ETFA", "ETFB", "ETFDH", "GALNS", "GBE1", "GLRA1", "GNS",
"ILK", "KIF20A", "LAMA4", "LYRM7", "MCM10", "NDUFA6", "NDUFA9",
"NDUFAF6", "NDUFAF8", "NEBL", "SPRED1", "TAB2", "TACO1", "TCAP",
"TGFB3", "TMPO", "TTC19", "UQCRB", "", "ACTC1", "ACTN2", "BAG3",
"CDH2", "DES", "DMD", "DOLK", "DSC2", "DSG2", "DSP", "EMD", "FLNC",
"JUP", "LAMP2", "LMNA", "MYBPC3", "MYH7", "NEXN", "NKX2-5", "PKP2",
"PLN", "RBM20", "RYR2", "SCN5A", "TMEM43", "TNNC1", "TNNI3",
"TNNI3K", "TNNT2", "TPM1", "TTN", "VCL", "ANK2", "ANKRD1", "CRYAB",
"CSRP3", "FKRP", "FKTN", "FLII", "GATA6", "LDB3", "MYH6", "MYLK3",
"MYPN", "NRAP", "PRDM16", "RHBDF1", "RPL3L", "SGCD", "SLC6A6",
"SPEG", "TBX20", "TBX5", "TCAP", "ABCC9", "EYA4", "FHOD3", "GATAD1",
"ABCC9", "ACTC1", "ACTN2", "BAG3", "CSRP3", "DES", "DMD", "DSP",
"EPG5", "EYA4", "HAMP", "HFE", "HFE2", "IDH2", "LMNA", "MYBPC3",
"MYH6", "MYH7", "NEXN", "PLN", "PPP1R13L", "RBM20", "SCN5A",
"SGCD", "SLC40A1", "SPEG", "TAZ", "TCAP", "TFR2", "TNNC1", "TNNI3",
"TNNT2", "TPM1", "TTN", "VCL", "ANKRD1", "CRYAB", "FKTN", "FLNC",
"GATAD1", "LDB3", "MYPN", "PRDM16", "PSEN1", "PSEN2", "SCN1B",
"ACTA1", "ALMS1", "CAVIN4", "CTF1", "DMPK", "DNAJC19", "DOLK",
"DSC2", "DSG2", "EMD", "FHL1", "FHL2", "GLA", "ILK", "JUP", "LAMA4",
"LAMP2", "MPO", "MYL2", "MYL3", "NEBL", "NKX2-5", "NPPA", "PDLIM3",
"PKP2", "PRKAG2", "RAB3GAP2", "RAF1", "RYR2", "SDHA", "SGCB",
"SYNE1", "SYNE2", "TBX20", "TMEM43", "TMPO", "TTR", "TXNRD2",
"XK", "ACTC1", "ACTN2", "CACNA1C", "CSRP3", "FHL1", "FHOD3",
"FLNC", "GLA", "JPH2", "LAMP2", "MYBPC3", "MYH7", "MYL2", "MYL3",
"PLN", "PRKAG2", "TNNC1", "TNNI3", "TNNT2", "TPM1", "TRIM63",
"TTR", "ALPK3", "ATAD3A", "GYG1", "MT-TI", "MYLK2", "MYPN", "ACADVL",
"ACTA1", "AGL", "ANKRD1", "ATP5E", "BRAF", "CALR3", "CASQ2",
"CAV3", "COA5", "CRYAB", "DES", "FOXRED1", "FXN", "GAA", "GLB1",
"GUSB", "HRAS", "KCNQ1", "KLF10", "LDB3", "LMNA", "LZTR1", "MAP2K1",
"MAP2K2", "MRPL3", "MT-TL1", "MYH6", "MYO6", "MYOM1", "MYOZ2",
"NEXN", "NRAS", "PDLIM3", "PTPN11", "RAF1", "SCO2", "SHOC2",
"SLC25A3", "SLC25A4", "SOS1", "TCAP", "TMEM70", "TSFM", "TTN",
"VCL", "ACTC1", "MYBPC3", "MYH7", "TAZ", "TNNT2", "TPM1", "CASQ2",
"DNAJC19", "DTNA", "LDB3", "LMNA", "MIB1", "MYPN", "PRDM16",
"SDHA", "TNNI3"), Panel = structure(c(1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L,
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L,
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L,
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L,
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 6L, 6L,
6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L), levels = c("Arrhythmogenic cardiomyopathy",
"Cardiomyopathies - including childhood onset", "Dilated cardiomyopathy - adult and teen",
"Dilated Cardiomyopathy and conduction defects", "Hypertrophic cardiomyopathy - teen and adult",
"Left Ventricular Noncompaction Cardiomyopathy"), class = "factor")), row.names = c(NA,
-468L), class = "data.frame")
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1条答案
按热度按时间ogsagwnx1#
在我看来,你在描述一个二分网络,其中面板是一个节点类型,基因是另一个。
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x1c 0d1x的数据
创建于2023-12-12带有reprex v2.0.2