Creating an interaction network in R

Question

[zizigolu]

Hello

I want to create an interaction network of mutations in terms of mutual exclusivity and co-occurance

I have this data

> dput(dat[1:5,])
structure(list(gene1 = c("XIRP2", "ABCA13", "VIRMA", "AHNAK2", 
"TPTE"), gene2 = c("CFAP54", "FAT3", "TENM4", "TP53", "CCDC168"
), pValue = c(0.0052991452991453, 0.0128205128205128, 0.0128205128205128, 
0.0257950744907267, 0.0299888517279821), oddsRatio = c(43.1892125950047, 
24.4044402363621, 24.4044402363621, Inf, 12.6559160941983), `00` = c(22L, 
21L, 21L, 9L, 20L), `11` = c(3, 3, 3, 8, 3), `01` = c(1, 2, 2, 
10, 2), `10` = c(1, 1, 1, 0, 2), Event = c("Co_Occurence", "Co_Occurence", 
"Co_Occurence", "Co_Occurence", "Co_Occurence"), pair = c("CFAP54, XIRP2", 
"ABCA13, FAT3", "TENM4, VIRMA", "AHNAK2, TP53", "CCDC168, TPTE"
), event_ratio = c("3/2", "3/3", "3/3", "8/10", "3/4")), row.names = c(NA, 
-5L), .internal.selfref = <pointer: 0x0000022bced61ef0>, class = c("data.table", 
"data.frame"))
>

And I need something like

I am wondering if there is any script to produce this from the data I have?

Thank you

[Ram]

You should take a look at the corrplot package. That might do the trick. If not, maybe ComplexHeatmap can help (althogh I don't know if CH can do upper triangle/lower triangle plots)

[Hamid Ghaedi]

If you have your data in maf format or you convert them into this format, maftools packages do such a job very well.

[zizigolu]

Thank you my data is in maf. I have two groups so that I want to create two plot with same order of genes but when I put my genes in order argument in maftools that returns an error so I am trying to create the interaction network myself