Unable to Assign Variable to Oncoplot Box Outline

[DarioS]

Apart from categories such as nonsense, missense there could an alternative way to categorise SNPs - before whole genome duplication, after whole genome duplication or indeterminate. About half of all cancer samples are estimated to have whole genome duplication. This could be represented as a border colour of the box in an oncoplot (the usual mutation categories are represented by box fill colours). Could a column in the data frame used to create MAF object be assigned to the box border colour?

[PoisonAlien]

I do not know how hard it can be because oncoplot is basically image command (not a grid). I will give it a try and let you know.

[DarioS]

That would be quite difficult in base graphics but easy using ggplot2.

[github-actions[bot]]

This issue is stale because it has been open for 60 days with no activity.

[DarioS]

I am still hopeful!

[SAADAT-Abu]

HI. As an oncoplot discussion is going on here. in the latest version (2.18). OncogenicPathways() function is replaced with pathways and I couldn't find a way to know which genes are present in the enriched pathway. I would be glad if someone can help me with this.

Thanks.

[PoisonAlien]

Hi,

Sorry for the confusion. Gene names are stored as an attribute of the output.

x = maftools::pathways(maf = laml)

attr(x, "genes")
$Cell_Cycle
 [1] "CDKN1A" "CDKN1B" "CDKN2A" "CDKN2B" "CDKN2C" "CCND1"  "CCND2"  "CCND3"  "CCNE1"  "CDK2"   "CDK4"   "CDK6"   "RB1"    "E2F1"   "E2F3"  

$Hippo
 [1] "STK4"   "STK3"   "SAV1"   "LATS1"  "LATS2"  "MOB1A"  "MOB1B"  "YAP1"   "WWTR1"  "TEAD1"  "TEAD2"  "TEAD3"  "TEAD4"  "PTPN14" "NF2"    "WWC1"   "TAOK1"  "TAOK2"  "TAOK3"  "CRB1"   "CRB2"  
[22] "CRB3"   "LLGL1"  "LLGL2"  "HMCN1"  "SCRIB"  "HIPK2"  "FAT1"   "FAT2"   "FAT3"   "FAT4"   "DCHS1"  "DCHS2"  "CSNK1E" "CSNK1D" "AJUBA"  "LIMD1"  "WTIP"  

$MYC
 [1] "MAX"    "MGA"    "MLX"    "MLXIP"  "MLXIPL" "MNT"    "MXD1"   "MXD3"   "MXD4"   "MXI1"   "MYC"    "MYCL"   "MYCN"  

$NOTCH
 [1] "ARRDC1" "CNTN6"  "CREBBP" "EP300"  "HES1"   "HES2"   "HES3"   "HES4"   "HES5"   "HEY1"   "HEY2"   "HEYL"   "KAT2B"  "KDM5A"  "NOTCH1" "NOTCH2" "NOTCH3" "NOTCH4" "NOV"    "NRARP"  "PSEN2" 
[22] "LFNG"   "ITCH"   "NCSTN"  "SPEN"   "JAG1"   "APH1A"  "FBXW7"  "FHL1"   "THBS2"  "HDAC2"  "MFAP2"  "CUL1"   "RFNG"   "NCOR1"  "NCOR2"  "MFAP5"  "HDAC1"  "NUMB"   "JAG2"   "MAML3"  "MFNG"  
[43] "CIR1"   "CNTN1"  "MAML1"  "MAML2"  "NUMBL"  "PSEN1"  "PSENEN" "RBPJ"   "RBPJL"  "RBX1"   "SAP30"  "SKP1"   "SNW1"   "CTBP1"  "CTBP2"  "ADAM10" "APH1B"  "ADAM17" "DLK1"   "DLL1"   "DLL3"  
[64] "DLL4"   "DNER"   "DTX1"   "DTX2"   "DTX3"   "DTX3L"  "DTX4"   "EGFL7" 

$NRF2
[1] "NFE2L2" "KEAP1"  "CUL3"  

$PI3K
 [1] "EIF4EBP1" "AKT1"     "AKT2"     "AKT3"     "AKT1S1"   "DEPDC5"   "DEPTOR"   "INPP4B"   "MAPKAP1"  "MLST8"    "MTOR"     "NPRL2"    "NPRL3"    "PDK1"     "PIK3CA"   "PIK3CB"   "PIK3R1"  
[18] "PIK3R2"   "PIK3R3"   "PPP2R1A"  "PTEN"     "RHEB"     "RICTOR"   "RPTOR"    "RPS6"     "RPS6KB1"  "STK11"    "TSC1"     "TSC2"    

$`RTK-RAS`
 [1] "ABL1"     "EGFR"     "ERBB2"    "ERBB3"    "ERBB4"    "PDGFRA"   "PDGFRB"   "MET"      "FGFR1"    "FGFR2"    "FGFR3"    "FGFR4"    "FLT3"     "ALK"      "RET"      "ROS1"     "KIT"     
[18] "IGF1R"    "NTRK1"    "NTRK2"    "NTRK3"    "SOS1"     "GRB2"     "PTPN11"   "KRAS"     "HRAS"     "NRAS"     "RIT1"     "ARAF"     "BRAF"     "RAF1"     "RAC1"     "MAP2K1"   "MAP2K2"  
[35] "MAPK1"    "NF1"      "RASA1"    "CBL"      "ERRFI1"   "CBLB"     "CBLC"     "INSR"     "INSRR"    "IRS1"     "SOS2"     "SHC1"     "SHC2"     "SHC3"     "SHC4"     "RASGRP1"  "RASGRP2" 
[52] "RASGRP3"  "RASGRP4"  "RAPGEF1"  "RAPGEF2"  "RASGRF1"  "RASGRF2"  "FNTA"     "FNTB"     "RCE1"     "ICMT"     "MRAS"     "PLXNB1"   "MAPK3"    "ARHGAP35" "RASA2"    "RASA3"    "RASAL1"  
[69] "RASAL2"   "RASAL3"   "SPRED1"   "SPRED2"   "SPRED3"   "DAB2IP"   "SHOC2"    "PPP1CA"   "SCRIB"    "PIN1"     "KSR1"     "KSR2"     "PEBP1"    "ERF"      "PEA15"    "JAK2"     "IRS2"    

$`TGF-Beta`
[1] "TGFBR1" "TGFBR2" "ACVR2A" "ACVR1B" "SMAD2"  "SMAD3"  "SMAD4" 

$TP53
[1] "TP53"    "MDM2"    "MDM4"    "ATM"     "CHEK2"   "RPS6KA3"

$WNT
 [1] "CHD8"   "LEF1"   "LGR4"   "LGR5"   "LRP5"   "LRP6"   "LZTR1"  "NDP"    "PORCN"  "RSPO1"  "SFRP1"  "SFRP2"  "SFRP4"  "SFRP5"  "SOST"   "TCF7L1" "TLE1"   "TLE2"   "TLE3"   "TLE4"   "WIF1"  
[22] "ZNRF3"  "CTNNB1" "DVL1"   "DVL2"   "DVL3"   "FRAT1"  "FRAT2"  "FZD1"   "FZD10"  "FZD2"   "FZD3"   "FZD4"   "FZD5"   "FZD6"   "FZD7"   "FZD8"   "FZD9"   "WNT1"   "WNT10A" "WNT10B" "WNT11" 
[43] "WNT16"  "WNT2"   "WNT3A"  "WNT4"   "WNT5A"  "WNT5B"  "WNT6"   "WNT7A"  "WNT7B"  "WNT8A"  "WNT8B"  "WNT9A"  "WNT9B"  "AMER1"  "APC"    "AXIN1"  "AXIN2"  "DKK1"   "DKK2"   "DKK3"   "DKK4"  
[64] "GSK3B"  "RNF43"  "TCF7"   "TCF7L2" "CHD4"  

# Then you can visualize your favorite pathways with oncoplot
maftools::oncoplot(maf = laml, pathways = 'sigpw', selectedPathways = c("RTK-RAS", "Cell_Cycle", "TP53"))

I hope this helps..

[SAADAT-Abu]

Thanks a lot.

[github-actions[bot]]

This issue is stale because it has been open for 60 days with no activity.

[github-actions[bot]]

This issue was closed because it has been inactive for 14 days since being marked as stale.