I am using Seurat object to use intra_netowrk function.
For example, when I run this intra_network function,
intra_network(goi = "VTN", data = g41.data, genes = g41.genes, cluster = g41.cluster, write = FALSE, plot = FALSE, species = c("homo sapiens"), coi = "cluster 2")
I got this:
Patwhay(s) that include VTN:
Syndecan interactions
ECM proteoglycans
Integrin cell surface interactions
Molecules associated with elastic fibres
[[1]]
a.gn b.gn nam location type
61095 ITGAV ITGB8 cluster 2 intra complex
61103 ITGAV ITGB1 cluster 2 intra complex
231930 LTBP3 TGFB3 cluster 2 intra complex
235835 FBLN1 MFAP1 cluster 2 intra complex
235840 FBLN1 VTN cluster 2 intra complex
Warning messages:
1: In shortest_paths(g.net.tmp, receptors, V(g.net.tmp)) :
At structural_properties.c:745 :Couldn't reach some vertices
2: In vattrs[[name]][index] <- value :
number of items to replace is not a multiple of replacement length
3: In par(opar) : graphical parameter "cin" cannot be set
4: In par(opar) : graphical parameter "cra" cannot be set
5: In par(opar) : graphical parameter "csi" cannot be set
6: In par(opar) : graphical parameter "cxy" cannot be set
7: In par(opar) : graphical parameter "din" cannot be set
8: In par(opar) : graphical parameter "page" cannot be set
What are those warning messages?
Also, why does it give intra network that not related to goi (VTN for this one).
I am using Seurat object to use intra_netowrk function.
For example, when I run this intra_network function, intra_network(goi = "VTN", data = g41.data, genes = g41.genes, cluster = g41.cluster, write = FALSE, plot = FALSE, species = c("homo sapiens"), coi = "cluster 2")
I got this: Patwhay(s) that include VTN:
Warning messages: 1: In shortest_paths(g.net.tmp, receptors, V(g.net.tmp)) : At structural_properties.c:745 :Couldn't reach some vertices 2: In vattrs[[name]][index] <- value : number of items to replace is not a multiple of replacement length 3: In par(opar) : graphical parameter "cin" cannot be set 4: In par(opar) : graphical parameter "cra" cannot be set 5: In par(opar) : graphical parameter "csi" cannot be set 6: In par(opar) : graphical parameter "cxy" cannot be set 7: In par(opar) : graphical parameter "din" cannot be set 8: In par(opar) : graphical parameter "page" cannot be set
What are those warning messages? Also, why does it give intra network that not related to goi (VTN for this one).