igraph : Invalid vertex names when using graph.edgelist and not graph_from_data_frame
Question
Depending on the fact I use one or the other following line of code, I get an error.
This one works well.
g <- igraph::graph_from_data_frame(d.int, directed = TRUE)
I got an error using this method to create an igraph object.
g <- igraph::graph.edgelist(as.matrix(unique(d.int[, c(1, 3)])), directed = FALSE)
Error is:
"Invalid vertex names"
Why?
The d.int dataframe (sif format) used with the second line is:
a.gn b.gn type
24115 KLRD1 CD3G controls-state-change-of
24132 KLRD1 FCGR1A controls-state-change-of
24150 KLRD1 TYROBP in-complex-with
28674 ITGA4 VCAM1 in-complex-with
28676 ITGA4 ITGB7 in-complex-with
28677 ITGA4 ITGAL controls-expression-of
28678 ITGA4 ITGB1 in-complex-with
30999 TYROBP CD3G controls-state-change-of
31018 TYROBP FCGR1A controls-state-change-of
44607 ITGAL ITGB2 in-complex-with
44608 ITGAL ITGA4 controls-expression-of
69420 CD300LB TYROBP in-complex-with
75890 B2M TYROBP in-complex-with
75905 B2M CD8A in-complex-with
75911 B2M CD3D in-complex-with
75915 B2M FCGR1A controls-state-change-of
75916 B2M KIR3DL1 in-complex-with
75919 B2M LILRB2 in-complex-with
75941 B2M CD3G in-complex-with
75942 B2M CD3G controls-state-change-of
75944 B2M HLA-G in-complex-with
75952 B2M HLA-F in-complex-with
75956 B2M LILRB1 in-complex-with
75970 B2M HLA-C in-complex-with
76007 B2M LILRA4 in-complex-with
76063 B2M HLA-A in-complex-with
76067 B2M KIR3DL2 in-complex-with
76086 B2M KLRC1 in-complex-with
76087 B2M HLA-B in-complex-with
76100 B2M KIR2DL3 in-complex-with
76114 B2M HLA-E in-complex-with
76128 B2M CD1D in-complex-with
76129 B2M KLRD1 in-complex-with
76130 B2M KIR2DL1 in-complex-with
76616 COL1A1 COL1A2 in-complex-with
78596 CD19 CD81 in-complex-with
78620 CD19 IFITM1 in-complex-with
78706 CD19 CD3G controls-state-change-of
78717 CD19 FCGR1A controls-state-change-of
88285 ICAM2 ITGAL in-complex-with
88286 ICAM2 ITGB2 in-complex-with
94075 ICAM3 ITGB2 in-complex-with
94076 ICAM3 ITGAL in-complex-with
101887 CD3D CD8A in-complex-with
101895 CD3D HLA-A in-complex-with
101915 CD3D CD3G in-complex-with
101916 CD3D HLA-G in-complex-with
101919 CD3D HLA-B in-complex-with
101926 CD3D HLA-F in-complex-with
101938 CD3D HLA-C in-complex-with
101961 CD3D HLA-E in-complex-with
109005 HLA-G LILRB2 in-complex-with
109024 HLA-G LILRA4 in-complex-with
109028 HLA-G LILRB1 in-complex-with
121205 CD3G HLA-A in-complex-with
121225 CD3G HLA-B in-complex-with
121281 CD3G FCGR1A in-complex-with
121297 CD3G HLA-G in-complex-with
121306 CD3G HLA-F in-complex-with
121317 CD3G HLA-C in-complex-with
121419 CD3G HLA-E in-complex-with
121456 CD3G CD8A in-complex-with
137496 CDH1 KLRG1 in-complex-with
137498 CDH1 ITGB7 in-complex-with
150270 HLA-A LILRB1 in-complex-with
150280 HLA-A LILRA4 in-complex-with
150287 HLA-A KIR3DL2 in-complex-with
150296 HLA-A LILRB2 in-complex-with
155691 CD200 CD200R1 in-complex-with
156706 ICAM1 ITGAL in-complex-with
156707 ICAM1 ITGB2 in-complex-with
157374 KLRC1 KLRD1 in-complex-with
168591 ITGB1 VCAM1 in-complex-with
179866 CD96 PVR in-complex-with
179910 KLRK1 TYROBP in-complex-with
179915 KLRK1 RAET1E in-complex-with
179921 KLRK1 CD3G controls-state-change-of
179937 KLRK1 FCGR1A controls-state-change-of
179980 KLRK1 MICB in-complex-with
180078 KLRK1 MICA in-complex-with
183355 CD1D CD3G in-complex-with
183360 CD1D CD3D in-complex-with
201658 ICAM4 ITGB2 in-complex-with
201659 ICAM4 ITGAL in-complex-with
227035 HLA-C LILRB2 in-complex-with
227037 HLA-C KIR2DL1 in-complex-with
227039 HLA-C LILRA4 in-complex-with
227055 HLA-C TYROBP in-complex-with
227056 HLA-C LILRB1 in-complex-with
227064 HLA-C KIR2DL3 in-complex-with
230227 HLA-B LILRA4 in-complex-with
230243 HLA-B KIR3DL1 in-complex-with
230245 HLA-B LILRB2 in-complex-with
230257 HLA-B LILRB1 in-complex-with
230258 HLA-B TYROBP in-complex-with
235388 CLEC2D KLRB1 in-complex-with
237811 C3 IFITM1 in-complex-with
237814 C3 CD19 in-complex-with
237820 C3 CD81 in-complex-with
237945 CD226 PVR in-complex-with
257417 CD81 IFITM1 in-complex-with
264111 ICAM5 ITGAL in-complex-with
264112 ICAM5 ITGB2 in-complex-with
285674 HLA-F LILRB2 in-complex-with
285682 HLA-F LILRA4 in-complex-with
285695 HLA-F LILRB1 in-complex-with
307587 CD99 PILRA in-complex-with
309539 HLA-E KLRD1 in-complex-with
309589 HLA-E KLRC1 in-complex-with
309610 HLA-E CD3G controls-state-change-of
309628 HLA-E FCGR1A controls-state-change-of
309629 HLA-E LILRB2 in-complex-with
309645 HLA-E TYROBP in-complex-with
309653 HLA-E LILRA4 in-complex-with
309698 HLA-E LILRB1 in-complex-with
341342 TREM1 TYROBP in-complex-with
342749 CD8A HLA-B in-complex-with
342752 CD8A HLA-A in-complex-with
342755 CD8A HLA-C in-complex-with
342756 CD8A HLA-F in-complex-with
342760 CD8A HLA-G in-complex-with
342761 CD8A HLA-E in-complex-with
360361 FCGR1A NCR3 in-complex-with
241501 TYROBP KLRD1 in-complex-with
286741 VCAM1 ITGA4 in-complex-with
286761 ITGB7 ITGA4 in-complex-with
286781 ITGB1 ITGA4 in-complex-with
446071 ITGB2 ITGAL in-complex-with
694201 TYROBP CD300LB in-complex-with
758901 TYROBP B2M in-complex-with
759051 CD8A B2M in-complex-with
759111 CD3D B2M in-complex-with
759161 KIR3DL1 B2M in-complex-with
759191 LILRB2 B2M in-complex-with
759411 CD3G B2M in-complex-with
759441 HLA-G B2M in-complex-with
759521 HLA-F B2M in-complex-with
759561 LILRB1 B2M in-complex-with
759701 HLA-C B2M in-complex-with
760071 LILRA4 B2M in-complex-with
760631 HLA-A B2M in-complex-with
760671 KIR3DL2 B2M in-complex-with
760861 KLRC1 B2M in-complex-with
760871 HLA-B B2M in-complex-with
761001 KIR2DL3 B2M in-complex-with
761141 HLA-E B2M in-complex-with
761281 CD1D B2M in-complex-with
761291 KLRD1 B2M in-complex-with
761301 KIR2DL1 B2M in-complex-with
766161 COL1A2 COL1A1 in-complex-with
785961 CD81 CD19 in-complex-with
786201 IFITM1 CD19 in-complex-with
882851 ITGAL ICAM2 in-complex-with
882861 ITGB2 ICAM2 in-complex-with
940751 ITGB2 ICAM3 in-complex-with
940761 ITGAL ICAM3 in-complex-with
1018871 CD8A CD3D in-complex-with
1018951 HLA-A CD3D in-complex-with
1019151 CD3G CD3D in-complex-with
1019161 HLA-G CD3D in-complex-with
1019191 HLA-B CD3D in-complex-with
1019261 HLA-F CD3D in-complex-with
1019381 HLA-C CD3D in-complex-with
1019611 HLA-E CD3D in-complex-with
1090051 LILRB2 HLA-G in-complex-with
1090241 LILRA4 HLA-G in-complex-with
1090281 LILRB1 HLA-G in-complex-with
1212051 HLA-A CD3G in-complex-with
1212251 HLA-B CD3G in-complex-with
1212811 FCGR1A CD3G in-complex-with
1212971 HLA-G CD3G in-complex-with
1213061 HLA-F CD3G in-complex-with
1213171 HLA-C CD3G in-complex-with
1214191 HLA-E CD3G in-complex-with
1214561 CD8A CD3G in-complex-with
1374961 KLRG1 CDH1 in-complex-with
1374981 ITGB7 CDH1 in-complex-with
1502701 LILRB1 HLA-A in-complex-with
1502801 LILRA4 HLA-A in-complex-with
1502871 KIR3DL2 HLA-A in-complex-with
1502961 LILRB2 HLA-A in-complex-with
1556911 CD200R1 CD200 in-complex-with
1567061 ITGAL ICAM1 in-complex-with
1567071 ITGB2 ICAM1 in-complex-with
1573741 KLRD1 KLRC1 in-complex-with
1685911 VCAM1 ITGB1 in-complex-with
1798661 PVR CD96 in-complex-with
1799101 TYROBP KLRK1 in-complex-with
1799151 RAET1E KLRK1 in-complex-with
1799801 MICB KLRK1 in-complex-with
1800781 MICA KLRK1 in-complex-with
1833551 CD3G CD1D in-complex-with
1833601 CD3D CD1D in-complex-with
2016581 ITGB2 ICAM4 in-complex-with
2016591 ITGAL ICAM4 in-complex-with
2270351 LILRB2 HLA-C in-complex-with
2270371 KIR2DL1 HLA-C in-complex-with
2270391 LILRA4 HLA-C in-complex-with
2270551 TYROBP HLA-C in-complex-with
2270561 LILRB1 HLA-C in-complex-with
2270641 KIR2DL3 HLA-C in-complex-with
2302271 LILRA4 HLA-B in-complex-with
2302431 KIR3DL1 HLA-B in-complex-with
2302451 LILRB2 HLA-B in-complex-with
2302571 LILRB1 HLA-B in-complex-with
2302581 TYROBP HLA-B in-complex-with
2353881 KLRB1 CLEC2D in-complex-with
2378111 IFITM1 C3 in-complex-with
2378141 CD19 C3 in-complex-with
2378201 CD81 C3 in-complex-with
2379451 PVR CD226 in-complex-with
2574171 IFITM1 CD81 in-complex-with
2641111 ITGAL ICAM5 in-complex-with
2641121 ITGB2 ICAM5 in-complex-with
2856741 LILRB2 HLA-F in-complex-with
2856821 LILRA4 HLA-F in-complex-with
2856951 LILRB1 HLA-F in-complex-with
3075871 PILRA CD99 in-complex-with
3095391 KLRD1 HLA-E in-complex-with
3095891 KLRC1 HLA-E in-complex-with
3096291 LILRB2 HLA-E in-complex-with
3096451 TYROBP HLA-E in-complex-with
3096531 LILRA4 HLA-E in-complex-with
3096981 LILRB1 HLA-E in-complex-with
3413421 TYROBP TREM1 in-complex-with
3427491 HLA-B CD8A in-complex-with
3427521 HLA-A CD8A in-complex-with
3427551 HLA-C CD8A in-complex-with
3427561 HLA-F CD8A in-complex-with
3427601 HLA-G CD8A in-complex-with
3427611 HLA-E CD8A in-complex-with
3603611 NCR3 FCGR1A in-complex-with
2 answers
solution1
1 ACCPTED 2021-12-10 09:04:42
The function igraph::graph.edgelist has the option el which should be a two column matrix. The two columns should contain node names for each side of the edge (eg from and to). You did d.int[, c(1, 3)] which selects the type which are not node names. Try d.int[, c(1, 2)] instead.
solution2
0 2021-12-10 09:30:53
I don't think there is any error at all when running
g <- igraph::graph.edgelist(as.matrix(unique(d.int[, c(1, 3)])), directed = FALSE)
plot(g)
Data
> dput(d.int)
structure(list(a.gn = c("KLRD1", "KLRD1", "KLRD1", "ITGA4", "ITGA4",
"ITGA4", "ITGA4", "TYROBP", "TYROBP", "ITGAL", "ITGAL", "CD300LB",
"B2M", "B2M", "B2M", "B2M", "B2M", "B2M", "B2M", "B2M", "B2M",
"B2M", "B2M", "B2M", "B2M", "B2M", "B2M", "B2M", "B2M", "B2M",
"B2M", "B2M", "B2M", "B2M", "COL1A1", "CD19", "CD19", "CD19",
"CD19", "ICAM2", "ICAM2", "ICAM3", "ICAM3", "CD3D", "CD3D", "CD3D",
"CD3D", "CD3D", "CD3D", "CD3D", "CD3D", "HLA-G", "HLA-G", "HLA-G",
"CD3G", "CD3G", "CD3G", "CD3G", "CD3G", "CD3G", "CD3G", "CD3G",
"CDH1", "CDH1", "HLA-A", "HLA-A", "HLA-A", "HLA-A", "CD200",
"ICAM1", "ICAM1", "KLRC1", "ITGB1", "CD96", "KLRK1", "KLRK1",
"KLRK1", "KLRK1", "KLRK1", "KLRK1", "CD1D", "CD1D", "ICAM4",
"ICAM4", "HLA-C", "HLA-C", "HLA-C", "HLA-C", "HLA-C", "HLA-C",
"HLA-B", "HLA-B", "HLA-B", "HLA-B", "HLA-B", "CLEC2D", "C3",
"C3", "C3", "CD226", "CD81", "ICAM5", "ICAM5", "HLA-F", "HLA-F",
"HLA-F", "CD99", "HLA-E", "HLA-E", "HLA-E", "HLA-E", "HLA-E",
"HLA-E", "HLA-E", "HLA-E", "TREM1", "CD8A", "CD8A", "CD8A", "CD8A",
"CD8A", "CD8A", "FCGR1A", "TYROBP", "VCAM1", "ITGB7", "ITGB1",
"ITGB2", "TYROBP", "TYROBP", "CD8A", "CD3D", "KIR3DL1", "LILRB2",
"CD3G", "HLA-G", "HLA-F", "LILRB1", "HLA-C", "LILRA4", "HLA-A",
"KIR3DL2", "KLRC1", "HLA-B", "KIR2DL3", "HLA-E", "CD1D", "KLRD1",
"KIR2DL1", "COL1A2", "CD81", "IFITM1", "ITGAL", "ITGB2", "ITGB2",
"ITGAL", "CD8A", "HLA-A", "CD3G", "HLA-G", "HLA-B", "HLA-F",
"HLA-C", "HLA-E", "LILRB2", "LILRA4", "LILRB1", "HLA-A", "HLA-B",
"FCGR1A", "HLA-G", "HLA-F", "HLA-C", "HLA-E", "CD8A", "KLRG1",
"ITGB7", "LILRB1", "LILRA4", "KIR3DL2", "LILRB2", "CD200R1",
"ITGAL", "ITGB2", "KLRD1", "VCAM1", "PVR", "TYROBP", "RAET1E",
"MICB", "MICA", "CD3G", "CD3D", "ITGB2", "ITGAL", "LILRB2", "KIR2DL1",
"LILRA4", "TYROBP", "LILRB1", "KIR2DL3", "LILRA4", "KIR3DL1",
"LILRB2", "LILRB1", "TYROBP", "KLRB1", "IFITM1", "CD19", "CD81",
"PVR", "IFITM1", "ITGAL", "ITGB2", "LILRB2", "LILRA4", "LILRB1",
"PILRA", "KLRD1", "KLRC1", "LILRB2", "TYROBP", "LILRA4", "LILRB1",
"TYROBP", "HLA-B", "HLA-A", "HLA-C", "HLA-F", "HLA-G", "HLA-E",
"NCR3"), b.gn = c("CD3G", "FCGR1A", "TYROBP", "VCAM1", "ITGB7",
"ITGAL", "ITGB1", "CD3G", "FCGR1A", "ITGB2", "ITGA4", "TYROBP",
"TYROBP", "CD8A", "CD3D", "FCGR1A", "KIR3DL1", "LILRB2", "CD3G",
"CD3G", "HLA-G", "HLA-F", "LILRB1", "HLA-C", "LILRA4", "HLA-A",
"KIR3DL2", "KLRC1", "HLA-B", "KIR2DL3", "HLA-E", "CD1D", "KLRD1",
"KIR2DL1", "COL1A2", "CD81", "IFITM1", "CD3G", "FCGR1A", "ITGAL",
"ITGB2", "ITGB2", "ITGAL", "CD8A", "HLA-A", "CD3G", "HLA-G",
"HLA-B", "HLA-F", "HLA-C", "HLA-E", "LILRB2", "LILRA4", "LILRB1",
"HLA-A", "HLA-B", "FCGR1A", "HLA-G", "HLA-F", "HLA-C", "HLA-E",
"CD8A", "KLRG1", "ITGB7", "LILRB1", "LILRA4", "KIR3DL2", "LILRB2",
"CD200R1", "ITGAL", "ITGB2", "KLRD1", "VCAM1", "PVR", "TYROBP",
"RAET1E", "CD3G", "FCGR1A", "MICB", "MICA", "CD3G", "CD3D", "ITGB2",
"ITGAL", "LILRB2", "KIR2DL1", "LILRA4", "TYROBP", "LILRB1", "KIR2DL3",
"LILRA4", "KIR3DL1", "LILRB2", "LILRB1", "TYROBP", "KLRB1", "IFITM1",
"CD19", "CD81", "PVR", "IFITM1", "ITGAL", "ITGB2", "LILRB2",
"LILRA4", "LILRB1", "PILRA", "KLRD1", "KLRC1", "CD3G", "FCGR1A",
"LILRB2", "TYROBP", "LILRA4", "LILRB1", "TYROBP", "HLA-B", "HLA-A",
"HLA-C", "HLA-F", "HLA-G", "HLA-E", "NCR3", "KLRD1", "ITGA4",
"ITGA4", "ITGA4", "ITGAL", "CD300LB", "B2M", "B2M", "B2M", "B2M",
"B2M", "B2M", "B2M", "B2M", "B2M", "B2M", "B2M", "B2M", "B2M",
"B2M", "B2M", "B2M", "B2M", "B2M", "B2M", "B2M", "COL1A1", "CD19",
"CD19", "ICAM2", "ICAM2", "ICAM3", "ICAM3", "CD3D", "CD3D", "CD3D",
"CD3D", "CD3D", "CD3D", "CD3D", "CD3D", "HLA-G", "HLA-G", "HLA-G",
"CD3G", "CD3G", "CD3G", "CD3G", "CD3G", "CD3G", "CD3G", "CD3G",
"CDH1", "CDH1", "HLA-A", "HLA-A", "HLA-A", "HLA-A", "CD200",
"ICAM1", "ICAM1", "KLRC1", "ITGB1", "CD96", "KLRK1", "KLRK1",
"KLRK1", "KLRK1", "CD1D", "CD1D", "ICAM4", "ICAM4", "HLA-C",
"HLA-C", "HLA-C", "HLA-C", "HLA-C", "HLA-C", "HLA-B", "HLA-B",
"HLA-B", "HLA-B", "HLA-B", "CLEC2D", "C3", "C3", "C3", "CD226",
"CD81", "ICAM5", "ICAM5", "HLA-F", "HLA-F", "HLA-F", "CD99",
"HLA-E", "HLA-E", "HLA-E", "HLA-E", "HLA-E", "HLA-E", "TREM1",
"CD8A", "CD8A", "CD8A", "CD8A", "CD8A", "CD8A", "FCGR1A"), type = c("controls-state-change-of",
"controls-state-change-of", "in-complex-with", "in-complex-with",
"in-complex-with", "controls-expression-of", "in-complex-with",
"controls-state-change-of", "controls-state-change-of", "in-complex-with",
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"in-complex-with", "in-complex-with", "in-complex-with", "in-complex-with",
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