Commit b9ecdc90 authored by mcariou's avatar mcariou
Browse files

update

parent 696188c4
x
ACADM
AGPS
CDK5RAP2
EDEM3
ERGIC1
GGH
GOLGA7
GRIPAP1
GRPEL1
IDE
IMPDH2
INHBE
ITGB1
LMAN2
MOV10
NUP214
POLA1
PRIM1
SLC27A2
SLC30A9
SLC44A2
TBK1
TOR1AIP1
VPS39
......@@ -157,9 +157,9 @@ sapply(seq(from=-0.5, to=5.5, by=1), function(x){
for (p in 0:5){
for (b in 0:5){
tmp<-tablo$`tmp$Gene.name`[tablo$nbats==b & tablo$nprimates==p]
if(length(tmp)>0 & length(tmp)<8){
if(length(tmp)>0 & length(tmp)<=8){
text(b,seq(from=(p-0.4), to=(p+0.4), length.out = length(tmp)), tmp, cex=0.4)
}else if (length(tmp)>8 & length(tmp)<16){
}else if (length(tmp)>8 & length(tmp)<=16){
print(c(p, b))
text((b-0.3),seq(from=(p-0.4), to=(p+0.4), length.out = 8), tmp[1:8], cex=0.4)
text((b+0.3),seq(from=(p-0.4), to=(p+0.4), length.out = (length(tmp)-8)), tmp[9:length(tmp)], cex=0.4)
......@@ -195,5 +195,14 @@ text(seq(from=0.1, to=1, length.out = length(tmp)-18),-2.8, tmp[19:length(tmp)],
@
<<>>=
write.csv(tablo[tablo$nbats>=3,"tmp$Gene.name"], "batssup3.csv", row.names=FALSE, quote=FALSE)
write.csv(tablo[tablo$nprimates>=3,"tmp$Gene.name"], "primatessup3.csv", row.names=FALSE, quote=FALSE)
write.csv(tablo, "primatesVbats.csv", row.names=FALSE, quote=FALSE)
@
\end{document}
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......@@ -437,9 +437,9 @@ Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
\hlkwa{for} \hlstd{(p} \hlkwa{in} \hlnum{0}\hlopt{:}\hlnum{5}\hlstd{)\{}
\hlkwa{for} \hlstd{(b} \hlkwa{in} \hlnum{0}\hlopt{:}\hlnum{5}\hlstd{)\{}
\hlstd{tmp}\hlkwb{<-}\hlstd{tablo}\hlopt{$}\hlstd{`tmp$Gene.name`[tablo}\hlopt{$}\hlstd{nbats}\hlopt{==}\hlstd{b} \hlopt{&} \hlstd{tablo}\hlopt{$}\hlstd{nprimates}\hlopt{==}\hlstd{p]}
\hlkwa{if}\hlstd{(}\hlkwd{length}\hlstd{(tmp)}\hlopt{>}\hlnum{0} \hlopt{&} \hlkwd{length}\hlstd{(tmp)}\hlopt{<}\hlnum{8}\hlstd{)\{}
\hlkwa{if}\hlstd{(}\hlkwd{length}\hlstd{(tmp)}\hlopt{>}\hlnum{0} \hlopt{&} \hlkwd{length}\hlstd{(tmp)}\hlopt{<=}\hlnum{8}\hlstd{)\{}
\hlkwd{text}\hlstd{(b,}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=(p}\hlopt{-}\hlnum{0.4}\hlstd{),} \hlkwc{to}\hlstd{=(p}\hlopt{+}\hlnum{0.4}\hlstd{),} \hlkwc{length.out} \hlstd{=} \hlkwd{length}\hlstd{(tmp)), tmp,} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
\hlstd{\}}\hlkwa{else if} \hlstd{(}\hlkwd{length}\hlstd{(tmp)}\hlopt{>}\hlnum{8} \hlopt{&} \hlkwd{length}\hlstd{(tmp)}\hlopt{<}\hlnum{16}\hlstd{)\{}
\hlstd{\}}\hlkwa{else if} \hlstd{(}\hlkwd{length}\hlstd{(tmp)}\hlopt{>}\hlnum{8} \hlopt{&} \hlkwd{length}\hlstd{(tmp)}\hlopt{<=}\hlnum{16}\hlstd{)\{}
\hlkwd{print}\hlstd{(}\hlkwd{c}\hlstd{(p, b))}
\hlkwd{text}\hlstd{((b}\hlopt{-}\hlnum{0.3}\hlstd{),}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=(p}\hlopt{-}\hlnum{0.4}\hlstd{),} \hlkwc{to}\hlstd{=(p}\hlopt{+}\hlnum{0.4}\hlstd{),} \hlkwc{length.out} \hlstd{=} \hlnum{8}\hlstd{), tmp[}\hlnum{1}\hlopt{:}\hlnum{8}\hlstd{],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
\hlkwd{text}\hlstd{((b}\hlopt{+}\hlnum{0.3}\hlstd{),}\hlkwd{seq}\hlstd{(}\hlkwc{from}\hlstd{=(p}\hlopt{-}\hlnum{0.4}\hlstd{),} \hlkwc{to}\hlstd{=(p}\hlopt{+}\hlnum{0.4}\hlstd{),} \hlkwc{length.out} \hlstd{= (}\hlkwd{length}\hlstd{(tmp)}\hlopt{-}\hlnum{8}\hlstd{)), tmp[}\hlnum{9}\hlopt{:}\hlkwd{length}\hlstd{(tmp)],} \hlkwc{cex}\hlstd{=}\hlnum{0.4}\hlstd{)}
......
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tmp$Gene.name,nbats,nprimates
AAR2,0,0
AASS,2,0
AATF,0,1
ACADM,4,5
ACSL3,0,1
ADAMTS1,0,0
AGPS,3,1
AKAP8L,0,1
ALG11,1,0
ALG5,0,2
ALG8,1,1
ANO6,2,2
AP2M1,0,1
ARF6,0,0
ATP13A3,0,2
ATP1B1,2,0
ATP6V1A,1,1
BCKDK,0,1
CCDC86,0,0
CDK5RAP2,3,5
CENPF,1,2
CEP112,1,1
CEP135,0,4
CEP250,1,2
CEP350,0,2
CEP68,1,5
CHMP2A,2,1
CHPF,0,2
CHPF2,1,1
CIT,1,2
CLCC1,0,1
CLIP4,2,4
CNTRL,1,3
COLGALT1,2,1
COMT,2,0
CSNK2A2,0,0
CSNK2B,0,1
CWC27,1,2
CYB5B,2,0
DCAF7,0,1
DCAKD,0,0
DCTPP1,0,0
DDX10,2,0
DNAJC11,1,0
DPH5,0,4
DPY19L1,0,0
ECSIT,0,0
EDEM3,5,3
EIF4H,0,0
EMC1,2,5
ERC1,1,1
ERGIC1,4,0
ERLEC1,0,2
ERMP1,2,0
ERP44,1,0
EXOSC2,0,3
EXOSC5,0,0
FAM162A,0,0
FAM98A,0,0
FAR2,2,2
FASTKD5,0,0
FBLN5,1,1
FBN2,2,2
FKBP10,1,0
FKBP15,0,0
FKBP7,0,2
FOXRED2,2,0
FYCO1,2,5
GCC1,1,0
GDF15,2,1
GFER,0,1
GGCX,1,0
GGH,5,5
GIGYF2,1,4
GLA,1,4
GNB1,0,1
GOLGA3,0,1
GOLGA7,5,5
GOLGB1,2,3
GORASP1,0,3
GRIPAP1,3,1
GRPEL1,3,0
HECTD1,2,5
HMOX1,1,1
HOOK1,0,0
HS2ST1,2,0
HSBP1,0,1
HYOU1,2,1
IDE,4,4
IL17RA,1,0
IMPDH2,4,1
INHBE,5,0
INTS4,1,0
ITGB1,4,5
LARP1,1,4
LARP7,0,3
LMAN2,4,4
LOX,1,1
MAP7D1,0,1
MDN1,2,3
MEPCE,2,0
MIB1,2,0
MOGS,0,0
MOV10,3,3
MRPS2,0,1
MRPS27,1,2
MRPS5,2,3
MYCBP2,2,5
NARS2,1,1
NDUFAF1,0,2
NDUFB9,0,4
NEK9,2,0
NEU1,2,0
NGDN,0,0
NGLY1,1,3
NLRX1,1,2
NOL10,1,1
NPC2,0,3
NUP210,2,2
NUP214,3,2
NUP98,0,1
OS9,0,0
PABPC4,1,2
PDZD11,0,1
PIGO,0,1
PIGS,0,0
PITRM1,1,3
PLAT,1,3
PLD3,0,1
PLEKHF2,2,0
POFUT1,2,1
POLA1,4,4
POLA2,1,0
POR,2,3
PPT1,1,0
PRIM1,3,2
PRKACA,1,0
PRKAR2A,1,4
PRKAR2B,1,2
PRRC2B,1,0
PSMD8,2,1
PTGES2,2,1
RAB10,0,0
RAB14,0,3
RAB2A,0,3
RAB5C,0,2
RAB7A,0,1
RAB8A,1,0
RAE1,1,1
RALA,0,0
RBM28,2,0
RBM41,0,2
RIPK1,2,4
RNF41,0,0
RTN4,1,2
SAAL1,1,4
SBNO1,2,2
SCAP,1,2
SDF2,0,0
SEPSECS,2,5
SIL1,1,0
SIRT5,1,4
SLC25A21,0,4
SLC27A2,5,4
SLC30A9,3,0
SLC44A2,5,0
SLU7,1,2
SMOC1,0,2
SRP54,0,0
SRP72,1,1
STC2,0,0
STOM,1,3
STOML2,0,0
SUN2,2,0
TAPT1,1,2
TARS2,0,1
TBK1,5,2
TBKBP1,0,2
THTPA,0,0
TIMM10,1,0
TIMM8B,0,3
TLE1,2,1
TM2D3,1,1
TMED5,2,0
TMEM39B,2,4
TMEM97,0,1
TOR1A,1,1
TOR1AIP1,5,5
TRIM59,0,3
TRMT1,1,3
TUBGCP2,0,4
TUBGCP3,2,1
TYSND1,2,0
UBAP2,0,4
UBAP2L,1,1
UBXN8,0,1
UGGT2,1,4
UPF1,0,0
USP54,1,3
VPS11,1,1
VPS39,5,5
ZC3H7A,1,1
ZDHHC5,1,2
ZNF318,0,5
ZNF503,0,1
ZYG11B,0,2
x
ACADM
CDK5RAP2
CEP135
CEP68
CLIP4
CNTRL
DPH5
EDEM3
EMC1
EXOSC2
FYCO1
GGH
GIGYF2
GLA
GOLGA7
GOLGB1
GORASP1
HECTD1
IDE
ITGB1
LARP1
LARP7
LMAN2
MDN1
MOV10
MRPS5
MYCBP2
NDUFB9
NGLY1
NPC2
PITRM1
PLAT
POLA1
POR
PRKAR2A
RAB14
RAB2A
RIPK1
SAAL1
SEPSECS
SIRT5
SLC25A21
SLC27A2
STOM
TIMM8B
TMEM39B
TOR1AIP1
TRIM59
TRMT1
TUBGCP2
UBAP2
UGGT2
USP54
VPS39
ZNF318
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