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Can we use our pre computed occurrence data to in maftools to plot Somatic Interaction?

Open kcmtest opened this issue 3 years ago • 0 comments

Describe the issue I would like to use the Somatic Interaction function of the maftools with my pre calculated data which was obtained from cbioportal

The small subset of my data looks like this

dput(head(a,20))
   structure(list(A = structure(c(4L, 34L, 13L, 13L, 26L, 26L, 18L, 
   37L, 26L, 18L, 51L, 37L, 44L, 26L, 18L, 51L, 41L, 26L, 18L, 51L
   ), .Label = c("ADAMTS15", "AFAP1L1", "ARHGEF15", "ATP6V0E2", 
   "BLID", "CADM1", "CASP1", "CAV2", "CBR1", "CD74", "CYP2E1", "EFNB3", 
   "ETS2", "FAM83G", "FLNC", "GALNS", "GBP6", "GFRA3", "GJC2", "GLB1L2", 
   "GPNMB", "GRAP", "HYOU1", "IGF2BP3", "IL12B", "JAKMIP2", "KCNIP1", 
   "KCNK1", "KCNMB1", "KIAA0087", "KIAA1549", "MICALL2", "MMP7", 
   "MX1", "NRGN", "OR2A9P", "OR9A4", "PATE2", "PATE4", "PCBP3", 
   "PCDH12", "PCDHB16", "PCDHGA3", "PDIA4", "PGBD5", "PRDM6", "PRR15", 
   "PRRT4", "PTGFR", "RARRES2", "RELL2", "RHOBTB3", "ROBO3", "RRAD", 
   "SCIN", "SCN4B", "SDR42E1", "SH3TC2", "SIDT2", "SLC22A4", "SLC28A3", 
   "SLC35F3", "SMO", "SNX24", "SORL1", "SPATA9", "THSD7A", "TLE1", 
   "TRIM36", "TRPM6", "UNCX", "VENTX", "VWA5A", "ZBTB46", "ZFHX3", 
   "ZNF853", "ZNRF1"), class = "factor"), B = structure(c(51L, 2L, 
   35L, 2L, 17L, 52L, 52L, 45L, 42L, 42L, 42L, 48L, 48L, 61L, 61L, 
   61L, 61L, 72L, 72L, 72L), .Label = c("AFAP1L1", "AGPAT3", "ARHGEF15", 
   "ATP6V0E2", "BLID", "CADM1", "CASP1", "CAV2", "CBR1", "CD74", 
   "CHRNB1", "CNIH3", "CRTAM", "FLNC", "GAS8", "GBP6", "GFRA3", 
   "GJC2", "GKAP1", "GLB1L2", "GPNMB", "GRAP", "HYOU1", "IGF2BP3", 
   "IL12B", "JAKMIP2", "KCNK1", "KCNMB1", "KIAA0087", "KIAA1549", 
   "LGALS9C", "MCOLN2", "MEST", "MMP7", "MX1", "NRGN", "NUDT7", 
   "OR2A9P", "PATE2", "PATE4", "PCBP3", "PCDH12", "PCDHGA12", "PCDHGA3", 
   "PDIA4", "PRDM6", "PRR15", "PRRT4", "PSAT1", "PTGFR", "RARRES2", 
   "RELL2", "RHOBTB3", "ROBO3", "RRAD", "SCIN", "SCN4B", "SDR42E1", 
   "SH3TC2", "SIDT2", "SLC22A4", "SLC29A4", "SLC35F3", "SMO", "SNX24", 
   "SORL1", "SOX18", "SPATA9", "SYCE1", "THSD7A", "TLE1", "TRIM36", 
   "UNCX", "UTF1", "VWA5A", "ZFHX3", "ZNF853"), class = "factor"), 
       Neither = c(185L, 185L, 183L, 183L, 186L, 186L, 186L, 186L, 
       186L, 186L, 186L, 186L, 186L, 186L, 186L, 186L, 186L, 186L, 
       186L, 186L), A.Not.B = c(0L, 0L, 2L, 2L, 0L, 0L, 0L, 0L, 
       0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), B.Not.A = c(0L, 
       0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
       0L, 0L, 0L, 0L), Both = c(6L, 6L, 6L, 6L, 5L, 5L, 5L, 5L, 
       5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L), Log2.Odds.Ratio = structure(c(1L, 
       1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
       1L, 1L, 1L, 1L), .Label = ">3", class = "factor"), p.Value = structure(c(1L, 
       1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
       1L, 1L, 1L, 1L), .Label = "<0.001", class = "factor"), q.Value = structure(c(1L, 
       1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
       1L, 1L, 1L, 1L), .Label = c("<0.001", "0.001", "0.003", "0.006", 
       "0.010", "0.012", "0.031"), class = "factor"), Tendency = structure(c(1L, 
       1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
       1L, 1L, 1L, 1L), .Label = "Co-occurrence", class = "factor")), row.names = c(NA, 
   20L), class = "data.frame")

I would like to generate similar plot like this , is it possible for me to do the same? using any function from maftools

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Command Please post your commands and the output (errors or any unexpected output)

Session info Run sessionInfo() and post the output below

kcmtest avatar Sep 24 '22 20:09 kcmtest