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Commit ea473043 authored by luppino's avatar luppino
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......@@ -44,27 +44,6 @@ db = merge(db,partners[,.(acc,pos,coupling_effect=partners_score)],by=
# db = db[,"imp_rs":=ifelse(site=="YES"|region=="YES","YES","NO")]
#
#
# db_site = fread("/Users/luppino/ownCloud/PhD_results/R workspace/train.o1047571",stringsAsFactors = F)
# db_site = merge(db_site,partners[,.(acc,pos,coupling_effect=partners_score)],by= c("acc","pos"),all.x = T)
# db_site = cbind(db_site,db$label1)
#
#
# db_site = db_site[,"region":=as.factor(ifelse(region=="NO","NO","YES"))]
# db_site = db_site[,"site":=as.factor(ifelse(site=="NO","NO","YES"))]
#
# db_site = db_site[,"imp_rs":=ifelse(site=="YES"|region=="YES","YES","NO")]
#
#
# par(mfrow=c(1,2),las=1,cex.axis=1.5,cex.lab=1.5,mar=c(4,5,4,4))
# b=barplot(table(db_site$imp_rs),ylim=c(0,10000),main="new annotations")
# text(b,y = table(db_site$site),labels = table(db_site$site),cex=1.3)
# b=barplot(table(db$site),ylim=c(0,10000),main="old annotations")
# text(b,y = table(db$site),labels = table(db$site),cex=1.3)
#
#
#
# #xlabs <- paste(levels(db$site),"\n(N=",table(db$label1,db$site),")",sep="")
#
# p1=ggplot(db_site,aes(x=imp_rs, y=coupling_effect)) +
# geom_violin() +
# geom_boxplot(width=0.1, color="black", alpha=0.2) +
......@@ -78,23 +57,7 @@ db = merge(db,partners[,.(acc,pos,coupling_effect=partners_score)],by=
# ) +
# xlab("UniProt sites and regions")+
# ylab("partners score")+
# stat_n_text(size=8)+ggtitle("")+
# facet_wrap(~V2,strip.position = "top",scales = "free_x")
# #scale_x_discrete(limits=c("NO","YES","NO","YES"),labels=xlabs)
#
# p2=ggplot(db,aes(x=site, y=coupling_effect)) +
# geom_violin() +
# geom_boxplot(width=0.1, color="black", alpha=0.2) +
# theme(legend.position = "none",plot.background = element_rect(fill = "white"),
# axis.text = element_text(size=15)
# ) +
# xlab("UniProt sites and regions")+
# ylab("partners score")+
# stat_n_text()+ggtitle("old annotations")
# #facet_wrap(~label1,strip.position = "top",scales = "free_x")
# #scale_x_discrete(limits=c("NO","YES","NO","YES"),labels=xlabs)
#
# grid.arrange(p1,p2,ncol=2)
# stat_n_text(size=8)+ggtitle("")
#
# ##########################################################################################
# #bootstrap analysis to check whether the partner score means are the same in the no and yes group of the site
......
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