Question

我有一个稀疏的200x200矩阵，只有8个边（非零权重）。图表＆＃34; rng＆＃34;有以下信息：

> rng
IGRAPH UNW- 200 8 -- 
+ attr: name (v/c), weight (e/n)
+ edges (vertex names):
[1] CDH1    --DLC1     CDH1    --KRTAP2.3 DLC1    --KRTAP2.3 DLC1    --NRG1    
[5] DLC1    --PODXL    DUSP5   --KRTAP2.3 ITGA6   --KRTAP2.3 KRTAP2.3--PODXL

您可以看到如上所示的8条边。但是，当绘图（rng）时，所有200个顶点都显示在图上。不知道为什么。 R脚本如下：

library("igraph");
pc<-read.table("my.network.txt", header = T, sep="  ", row.names="GENE_ID");
rng <- graph_from_adjacency_matrix(as.matrix(pc), weighted = TRUE, mode = "undirected");
plot(rng);

文件＆＃34; my.network.txt＆＃34;如下：

GENE_ID ADAM10  ADAMTS12    ADRB2   ALDH1A3 ALDH1B1 ALDH3B1 ALPP    ANKRD29 ANO2    ANXA8L2 ARHGDIB ARHGEF2 ARL4C   ARRDC3  ASNS    ATF3    ATP7B   B4GALT5 BAMBI   BCAN    BCL11A  C1orf21 CAPN6   CASP3   CAV1    CAV2    CCDC64  CCND1   CCNJL   CDH1    CDK14   CDK18   CDKN2B  CLIC4   CLPTM1L CLSTN2  COL4A4  COL5A1  COL5A3  COL7A1  CPE CTGF    CTSL2   CXCR7   CYBRD1  DAPK1   DCLK1   DHRS3   DIO2    DKK1    DLC1    DNAH5   DNM3    DOCK10  DOCK4   DSC2    DSC3    DUSP5   DUSP6   DUSP7   DUSP8   EFR3B   EHD2    EPAS1   ERAP2   ETV4    ETV5    F3  FAM84A  FAM84B  FBN1    FBXL2   FHL1    FRMD3   FSTL1   FTSJ1   FYN FZD4    GLRB    GPR3    GPRC5A  GPRC5B  GREB1L  HBEGF   HMGA1   HPS5    HSF2BP  HTR7    IFI6    IGFBP7  IGFBPL1 IL32IRF9    ITGA6   JAK1    KCNB1   KCNIP1  KIAA1462    KIAA1549L   KRT17   KRTAP2-3    LBH LDLR    LOC100287314    LOC100506895    LOC400680   LOC440028   LOC645638   LOC728752   LOXL4   MAMDC2  MFAP5   MME MMP19   MX1 MYL9    MYLK    NDRG1   NMT2    NNMT    NRG1    NT5E    NTN4    OLFM1   OLFM2   OLFML2A OXTR    PAPL    PCDH20  PDLIM1  PER2PIK3R3  PLA2R1  PLAC8   PLAU    PLCB4   PLD1    PLEKHG4B    PLEKHH2 PLSCR4  PLXNA2  PLXNC1  PNPLA3  PODXL   PRICKLE1    PRKCH   PROS1   PRPS1   PRR16   PRSS23  PSAT1   PSG1    PSG4PSG7    PTGES   RAB11FIP1   RASA3   RBM24   S100A2  SCARA3  SDC4    SDHAP3  SEMA5A  SHISA2  SIPA1L2 SLC7A2  SNCAIP  SORL1   SOX9    STX11   STX3    SYN2    SYPL2   TAGLN   TGFB2   TGM2THBD    THBS1   TIAM2   TM4SF1  TMEM178B    TMEM2   TMSB4X  TNNC1   TNNT2   TNS3    TP53I11 TP53INP1    TTC9    TUBA1A  UGCG    UPP1    WDFY2   ZFP82   ZNF114  ZNF185  ZNF430  ZNF431  ZNF562  ZNF566
ADAM10  0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0 ...
ADAMTS12    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   ...
.
.
.

这很奇怪。

Answer 1

图中没有边的顶点仍然是图中的顶点...您可能想要删除度数小于1的所有顶点：

> g2 = delete.vertices(g,degree(g)<1)
> plot(g2)

即使有一些边缘，igraph也会在绘图上显示所有顶点

1 个答案: