Given a surrogateTable object generated by buildSurrogateTable(), generate all surrogate graphs.
plotAllGraphs(surrogateTable, gisticCopyCalls, surrogateResults, intome)
| surrogateTable | A surrogateTable data frame generated from buildSurrogateTable() |
|---|---|
| gisticCopyCalls | When set to NULL, plotAllGraphs will look in the surrogateResults$mutCopyFrames object for the copy number calls for each gene. |
| surrogateResults | |
| intome |
An SVG file generated for each line in the surrogateTable data frame. The SVG files will have the format (Sample)-GeneName.svg.
##---- Should be DIRECTLY executable !! ---- ##-- ==> Define data, use random, ##-- or do help(data=index) for the standard data sets. ##load surrogate result object library(DLBCL) data(interactome) data(surrogateResult) surrogateTable <- buildSurrogateTable(surrogateResult) ##filter the surrogate table based on p-value and return surrogate mutations greater than 5. filteredSurrTable <- surrogateTable[surrogateTable$pvalue < 0.05 & surrogateTable$neighbor > 3,] filteredSurrTable#> ID Gene Sample NodeName #> TCGA.AO.A12D-IRS2 TCGA.AO.A12D-IRS2 IRS2 TCGA.AO.A12D IRS2(8660) #> TCGA.AO.A12D-PIK3R3 TCGA.AO.A12D-PIK3R3 PIK3R3 TCGA.AO.A12D PIK3R3(8503) #> TCGA.AO.A12D-RAF1 TCGA.AO.A12D-RAF1 RAF1 TCGA.AO.A12D RAF1(5894) #> TCGA.AO.A12D-SKP2 TCGA.AO.A12D-SKP2 SKP2 TCGA.AO.A12D SKP2(6502) #> TCGA.AO.A12D-SMARCA4 TCGA.AO.A12D-SMARCA4 SMARCA4 TCGA.AO.A12D SMARCA4(6597) #> TCGA.AO.A12D-YWHAE TCGA.AO.A12D-YWHAE YWHAE TCGA.AO.A12D YWHAE(7531) #> TCGA.BH.A0DS-CSNK2A1 TCGA.BH.A0DS-CSNK2A1 CSNK2A1 TCGA.BH.A0DS CSNK2A1(1457) #> TCGA.BH.A0DS-GSK3B TCGA.BH.A0DS-GSK3B GSK3B TCGA.BH.A0DS GSK3B(2932) #> TCGA.BH.A0DS-GTF2H1 TCGA.BH.A0DS-GTF2H1 GTF2H1 TCGA.BH.A0DS GTF2H1(2965) #> TCGA.BH.A0DS-IRS4 TCGA.BH.A0DS-IRS4 IRS4 TCGA.BH.A0DS IRS4(8471) #> TCGA.BH.A0DS-MAPK14 TCGA.BH.A0DS-MAPK14 MAPK14 TCGA.BH.A0DS MAPK14(1432) #> TCGA.E2.A1B5-GSK3B TCGA.E2.A1B5-GSK3B GSK3B TCGA.E2.A1B5 GSK3B(2932) #> TCGA.E2.A1B5-GTF2H1 TCGA.E2.A1B5-GTF2H1 GTF2H1 TCGA.E2.A1B5 GTF2H1(2965) #> TCGA.E2.A1B5-HDAC3 TCGA.E2.A1B5-HDAC3 HDAC3 TCGA.E2.A1B5 HDAC3(8841) #> TCGA.E2.A1B5-HSPCA TCGA.E2.A1B5-HSPCA HSPCA TCGA.E2.A1B5 HSPCA(3320) #> TCGA.E2.A1B5-MAPK8 TCGA.E2.A1B5-MAPK8 MAPK8 TCGA.E2.A1B5 MAPK8(5599) #> TCGA.E2.A1B5-PDGFRB TCGA.E2.A1B5-PDGFRB PDGFRB TCGA.E2.A1B5 PDGFRB(5159) #> TCGA.E2.A1B5-PTK2 TCGA.E2.A1B5-PTK2 PTK2 TCGA.E2.A1B5 PTK2(5747) #> TCGA.E2.A1B5-UBB TCGA.E2.A1B5-UBB UBB TCGA.E2.A1B5 UBB(7314) #> neighbor degree pvalue isMutated #> TCGA.AO.A12D-IRS2 4 35 0.025 1 #> TCGA.AO.A12D-PIK3R3 4 11 0.000 0 #> TCGA.AO.A12D-RAF1 7 89 0.023 0 #> TCGA.AO.A12D-SKP2 5 25 0.002 0 #> TCGA.AO.A12D-SMARCA4 5 36 0.004 0 #> TCGA.AO.A12D-YWHAE 7 58 0.001 0 #> TCGA.BH.A0DS-CSNK2A1 14 159 0.009 0 #> TCGA.BH.A0DS-GSK3B 6 59 0.028 0 #> TCGA.BH.A0DS-GTF2H1 4 26 0.014 0 #> TCGA.BH.A0DS-IRS4 4 14 0.002 0 #> TCGA.BH.A0DS-MAPK14 7 76 0.043 0 #> TCGA.E2.A1B5-GSK3B 5 59 0.035 0 #> TCGA.E2.A1B5-GTF2H1 4 26 0.007 0 #> TCGA.E2.A1B5-HDAC3 5 57 0.028 0 #> TCGA.E2.A1B5-HSPCA 6 74 0.019 0 #> TCGA.E2.A1B5-MAPK8 6 63 0.005 0 #> TCGA.E2.A1B5-PDGFRB 4 53 0.046 0 #> TCGA.E2.A1B5-PTK2 6 81 0.020 0 #> TCGA.E2.A1B5-UBB 5 55 0.022 0#plot all graphs in current working directory #be careful with the size of the table you pass to plotAllGraphs - it may generate #a huge number of files. plotAllGraphs(filteredSurrTable, surrogateResult, intome=interactome)#> [1] "IRS2(8660) TCGA.AO.A12D"#> Error in renderSubNetSimple(NodeName, Sample, GeneName, intome, gisticCopyCalls = NULL, resultObj = surrogateResults): object 'geneIntTable' not found