Oncoprint gives Out of Memory Error for large number of samples and genes

[inodb]

From Evan Seffar for MSK Portal:

Step 1 : Cbioportal Study Link : 900 pts / samples ~
https://bit.ly/3Bctu90
Step 2 : Query a gene : MDM2 for example
https://bit.ly/4ehRvul
Step 3 : Paste the Pathways (290 genes) and click on submit query

Note that Evan tested on public and GENIE portal where this does not seem to be an issue

["TP53"
TP53
MDM2
MDM4
ATM
CHEK2
RPS6KA3]

["CELL-CYCLE" 
CDKN1A
CDKN1B
CDKN2A
CDKN2B
CDKN2C
CCND1
CCND2
CCND3
CCNE1
CDK2
CDK4
CDK6
RB1
E2F1
E2F3
]

["Epigenetic"
ASXL1
DNMT3A
EED
EZH2
JAK2
NCOR1
ARID1A
ASXL2
ATRX
BCOR
BRD4
CARM1
CREBBP
DAXX
DNMT1
DNMT3B
DOT1L
EP300
EZH1
KDM5A
KDM5C
KDM6A
MEN1
NCOA3
NSD1
PBRM1
SETD2
SMARCA4
SMARCD1
SMYD3
SUZ12
TET1
TET2
HIST1H3B
NSD3
ARID1B
ARID2
CTCF
H3F3A
H3F3B
H3F3C
HIST1H1C
HIST1H2BD
HIST1H3A
HIST1H3C
HIST1H3D
HIST1H3E
HIST1H3F
HIST1H3G
HIST1H3H
HIST1H3I
HIST1H3J
HIST2H3C
HIST2H3D
HIST3H3
IDH1
IDH2
KMT2A
KMT2B
KMT2C
KMT2D
KMT5A
NSD2
SMARCB1
]


["RAS-RAF" 
KRAS
HRAS
NRAS
RIT1
ARAF
BRAF
RAF1
RAC1
MAP2K1
MAP2K2
MAPK1
NF1
RASA1
CBL
ERRFI1
SPRED1
ERF
JAK2
IRS2
]

["DDR"
NTHL1
POLD1
ATM
ATR
BABAM1
BARD1
BLM
BRCA1
BRCA2
BRIP1
CHEK1
CHEK2
ERCC2
ERCC3
ERCC4
ERCC5
FANCA
FANCC
MDC1
MLH1
MSH2
MSH3
MSH6
MUTYH
NBN
PALB2
PARP1
PMS1
PMS2
POLE
RAD21
RAD50
RAD51
RAD51B
RAD51C
RAD51D
RAD52
RAD54L
RECQL
RECQL4
RTEL1
SLX4
TP53BP1
XRCC2
]

["RTK" 
EGFR
ERBB2
ERBB3
ERBB4
PDGFRA
PDGFRB
MET
FGFR1
FGFR2
FGFR3
FGFR4
FLT3
ALK
RET
ROS1
KIT
IGF1R
NTRK1
NTRK3
SOS1
PTPN11]

[
"PI3K"
AKT1
AKT2
AKT3
INPP4B
MLST8
MTOR
NPRL2
NPRL3
PIK3CA
PIK3CB
PIK3R1
PIK3R2
PIK3R3
PPP2R1A
PTEN
RHEB
RICTOR
RPTOR
RPS6KB1
STK11
TSC1
TSC2
]



["HIPPO" 
MST1
STK3
SAV1
LATS1
LATS2
MOB1A
MOB1B
YAP1
TEAD2
PTPN14
NF2
WWC1
TAOK1
TAOK2
TAOK3
CRB1
CRB2
LLGL1
LLGL2
HMCN1
FAT1
FAT2
FAT3
FAT4
DCHS1
DCHS2
CSNK1E
CSNK1D
]

["MYC" 
MAX
MGA
MLX
MNT
MXI1
MYC
MYCN
]

["NOTCH" 
ARRDC1
CNTN6
CREBBP
EP300
HES1
HES2
HES3
HES4
HES5
HEY1
HEY2
HEYL
KAT2B
KDM5A
NOTCH1
NOTCH2
NOTCH3
NOTCH4
CCN3
NRARP
PSEN2
SPEN
FBXW7
CUL1
NCOR1
NCOR2
JAG2
MAML3
DNER
]

["NRF2"
NFE2L2
KEAP1
CUL3
]


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




["WNT"
SFRP1
SFRP2
SFRP4
SFRP5
SOST
TCF7L1
TLE1
TLE2
TLE3
TLE4
WIF1
ZNRF3
CTNNB1
AMER1
APC
AXIN1
AXIN2
DKK1
DKK2
DKK3
DKK4
GSK3B
RNF43
TCF7
TCF7L2
]