diff --git a/batssup3.csv b/batssup3.csv new file mode 100644 index 0000000000000000000000000000000000000000..e6bfe05d77b2f0c7ce293f7c50ea5a1c349b8880 --- /dev/null +++ b/batssup3.csv @@ -0,0 +1,25 @@ +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 diff --git a/covid_comp_dataset.Rnw b/covid_comp_dataset.Rnw index bafcbd75fc65cbb53b296a99d2f9ddfd8ba33827..fd6bce59cc48feffd0f93aa39ec8a68401f8bc3e 100644 --- a/covid_comp_dataset.Rnw +++ b/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} diff --git a/covid_comp_dataset.pdf b/covid_comp_dataset.pdf index 867466467d85fd6f3d7df8bec56751c14e922cb5..fc063a0a4ca9242251be989b07346ca95ed84b49 100644 Binary files a/covid_comp_dataset.pdf and b/covid_comp_dataset.pdf differ diff --git a/covid_comp_dataset.tex b/covid_comp_dataset.tex index 1b3153d7467c01b7db2e2732118e40a0c6eb40a2..4996449c7a8c16ce05b8a0d510d398997a801063 100644 --- a/covid_comp_dataset.tex +++ b/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{)} diff --git a/figure/mondrianbats-1.pdf b/figure/mondrianbats-1.pdf index ac09711bd0b2bede7ad26d46dd53fa1d689edf57..7949668e117a2e818cefb3615526fcf1bf197353 100644 Binary files a/figure/mondrianbats-1.pdf and b/figure/mondrianbats-1.pdf differ diff --git a/figure/mondrianbats-2.pdf b/figure/mondrianbats-2.pdf index 2a4011da959a21d438446a622c6deaba5d742290..0ed4dc43dc2559639055af5260853cd9b244ac27 100644 Binary files a/figure/mondrianbats-2.pdf and b/figure/mondrianbats-2.pdf differ diff --git a/figure/subsetbats-1.pdf b/figure/subsetbats-1.pdf index 49be00883d055eb066ccc440f47ce6effaf4ed24..3bde3778cbe329fcad729111ff19bca9dc8ac061 100644 Binary files a/figure/subsetbats-1.pdf and b/figure/subsetbats-1.pdf differ diff --git a/figure/subsetbats-2.pdf b/figure/subsetbats-2.pdf index 590495c15e06dc1b0bee2f76cea71f81d5309f79..92c427df1256950e48317fc4fc0e208d30611a75 100644 Binary files a/figure/subsetbats-2.pdf and b/figure/subsetbats-2.pdf differ diff --git a/figure/subsetbats-3.pdf b/figure/subsetbats-3.pdf index 568a0cf23c38b5b96f88cf9a92276dfd4a64ac3a..c7acf8a98e5bdbe9169d6a981d276353b0b2a969 100644 Binary files a/figure/subsetbats-3.pdf and b/figure/subsetbats-3.pdf differ diff --git a/figure/tablo-1.pdf b/figure/tablo-1.pdf index 81dfdc36c4ec70c19d061880910080908798af9a..000e81a5aed6de57946c2c93e27ba1b06dfa6b3c 100644 Binary files a/figure/tablo-1.pdf and b/figure/tablo-1.pdf differ diff --git a/primatesVbats.csv b/primatesVbats.csv new file mode 100644 index 0000000000000000000000000000000000000000..cb3da3cb58d8d5b88272de4608550a7ffb6cb0c9 --- /dev/null +++ b/primatesVbats.csv @@ -0,0 +1,207 @@ +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 diff --git a/primatessup3.csv b/primatessup3.csv new file mode 100644 index 0000000000000000000000000000000000000000..6ec20d03f7c8285faaa81ced23966452c5755518 --- /dev/null +++ b/primatessup3.csv @@ -0,0 +1,56 @@ +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