update

batssup3.csv

+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

covid_comp_dataset.Rnw

@@ -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}
 

covid_comp_dataset.tex

@@ -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{)}

primatesVbats.csv

+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

primatessup3.csv

+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