Commit fbde95f6 authored by your name's avatar your name
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new dginn file format 4 bats + mondrian plots

parent 536f7819
......@@ -341,6 +341,21 @@ n12, n23, n13, n123,
category=c("DGINN-Young-primate", "Young-primate", "Cooper-primate"))
@
\subsection{Mondrian}
<<mondrianprimates>>=
library(Mondrian)
monddata<-as.data.frame(tmp$Gene.name)
monddata$primates_dginn_young<-ifelse(tmp$PosSel_PamlM7M8=="Y", 1,0)
monddata$primates_young<-ifelse(tmp$pVal.M8vsM7<0.05, 1, 0)
monddata$primates_cooper<-ifelse(tmp$cooper.primates.M7.M8_p_val<0.05, 1, 0)
mondrian(monddata[,2:4])
@
%\subsection{Comparaison des codons?}
%Subtable with lines with both methods showing positive selection.
......@@ -405,9 +420,21 @@ listjoined<-mapply(c, listdginn, listjanet, SIMPLIFY=FALSE)
Lecture du tableau.
<<readtab4test, eval=F>>=
# Tableau tel qu'il est à cet étape du script, pour travailler sur l'ajout du nouveau tableau bats sans recommencer au début à chaque fois.
tab<-read.delim("COVID_PAMLresults_332hits_plusBatScreens_plusDGINN_20200506.txt",
header=TRUE, sep="\t")
@
<<>>=
dginnbats<-read.delim("/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/data/2020_bats_completeResults.csv",
#dginnbatsold<-read.delim("/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/data/2020_bats_completeResults.csv",
# fill=T, h=T)
dginnbats<-read.delim("/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/data/DGINN_202005281339summary_cleaned.tab",
fill=T, h=T)
dim(dginnbats)
names(dginnbats)
length(unique(dginnbats$Gene))
......@@ -425,42 +452,9 @@ Merge tables:
<<bats>>=
add_col<-function(dginnfile=dginnbats, method="PamlM1M2", prefixe="bats_"){
tmp<-dginn[dginnfile$Method==method,
c("Gene", "Omega", "PosSel", "PValue", "NbSites", "PSS")]
names(tmp)<-c("cooper.batsGene", paste0(prefixe, "Omega_", method),
paste0(prefixe, "PosSel_", method), paste0(prefixe, "PValue_", method),
paste0(prefixe, "NbSites_", method), paste0(prefixe, "PSS_", method))
tab<-merge(tab, tmp, by="cooper.batsGene", all.x=T)
return(tab)
}
tab<-add_col(dginnfile=dginnbats, method="PamlM1M2", prefixe="bats_")
names(dginnbats)<-c("File", "bats_Name", "cooper.batsGene", paste0("bats_", names(dginnbats)[-(1:3)]))
tab<-add_col(dginnfile=dginnbats, method="PamlM7M8", prefixe="bats_")
tab<-add_col(dginnfile=dginnbats, method="BppM1M2", prefixe="bats_")
tab<-add_col(dginnfile=dginnbats, method="BppM7M8", prefixe="bats_")
head(na.omit(tab[, c("cooper.batsGene", "cooper.batsAverage_dNdS","cooper.batsM7.M8_p_value", "bats_Omega_PamlM7M8","bats_PValue_PamlM7M8")]))
# Manip pour la colonne BUSTED
tmp<-dginn[dginn$Method=="BUSTED",c("Gene", "Omega", "PosSel", "PValue")]
names(tmp)<-c("cooper.batsGene", "bats_Omega_BUSTED", "bats_PosSel_BUSTED", "bats_PValue_BUSTED")
tab<-merge(tab, tmp, all.x=T, by="cooper.batsGene")
tmp<-dginn[dginn$Method=="MEME",c("Gene", "NbSites", "PSS")]
names(tmp)<-c("cooper.batsGene", "bats_NbSites_MEME", "bats_PSS_MEME")
tab<-merge(tab, tmp, all.x=T, by="cooper.batsGene")
dim(tab)
tab<-merge(tab,dginnbats, by="cooper.batsGene", all.x=T)
@
......@@ -470,22 +464,23 @@ dim(tab)
<<omegaM7M8bats>>=
plot(tab$cooper.batsAverage_dNdS, tab$bats_Omega_PamlM7M8,
plot(tab$cooper.batsAverage_dNdS, tab$bats_omegaM0codeml,
xlab="Omega Cooper-bats", ylab="Omega DGINN-bats")
@
\subsubsection{pvalues pour M7M8}
<<pvalM7M8bats>>=
tab$bats_codemlM7M8.p.value<-as.numeric(as.character(tab$bats_codemlM7M8.p.value))
plot(tab$cooper.batsM7.M8_p_value, tab$bats_PValue_PamlM7M8, pch=20,
plot(tab$cooper.batsM7.M8_p_value, tab$bats_codemlM7M8.p.value, pch=20,
xlab="p-value Cooper-bats", ylab="p-value DGINN-bats", main="M7vM8 Paml")
points(tab$cooper.batsM7.M8_p_value[tab$cooper.batsM7.M8_p_value>0.05 & tab$bats_PValue_PamlM7M8<0.05],
tab$bats_PValue_PamlM7M8[tab$cooper.batsM7.M8_p_value>0.05 & tab$bats_PValue_PamlM7M8<0.05],
points(tab$cooper.batsM7.M8_p_value[tab$cooper.batsM7.M8_p_value>0.05 & tab$bats_codemlM7M8.p.value<0.05],
tab$bats_codemlM7M8.p.value[tab$cooper.batsM7.M8_p_value>0.05 & tab$bats_codemlM7M8.p.value<0.05],
col="red", pch=20)
points(tab$cooper.batsM7.M8_p_value[tab$cooper.batsM7.M8_p_value<0.05 & tab$bats_PValue_PamlM7M8>0.05],
tab$bats_PValue_PamlM7M8[tab$cooper.batsM7.M8_p_value<0.05 & tab$bats_PValue_PamlM7M8>0.05],
points(tab$cooper.batsM7.M8_p_value[tab$cooper.batsM7.M8_p_value<0.05 & tab$bats_codemlM7M8.p.value>0.05],
tab$bats_codemlM7M8.p.value[tab$cooper.batsM7.M8_p_value<0.05 & tab$bats_codemlM7M8.p.value>0.05],
col="green", pch=20)
......@@ -531,17 +526,17 @@ legend("topleft", c("<0.05 in Hawkins but >0.05 in Cooper",
<<pvalM7M8compautre>>=
plot(tab$hawkins_Positive.Selection..M8vM8a.p.value, tab$bats_PValue_PamlM7M8,
plot(tab$hawkins_Positive.Selection..M8vM8a.p.value, tab$bats_codemlM7M8.p.value,
pch=20, xlab="p-value hawkins-bats", ylab="p-value DGINN-bats", main="M7vM8 Paml")
points(tab$hawkins_Positive.Selection..M8vM8a.p.value[tab$hawkins_Positive.Selection..M8vM8a.p.value>0.05 &
tab$bats_PValue_PamlM7M8<0.05],
tab$bats_PValue_PamlM7M8[tab$hawkins_Positive.Selection..M8vM8a.p.value>0.05 &
tab$bats_PValue_PamlM7M8<0.05], col="red", pch=20)
tab$bats_codemlM7M8.p.value<0.05],
tab$bats_codemlM7M8.p.value[tab$hawkins_Positive.Selection..M8vM8a.p.value>0.05 &
tab$bats_codemlM7M8.p.value<0.05], col="red", pch=20)
points(tab$hawkins_Positive.Selection..M8vM8a.p.value[tab$hawkins_Positive.Selection..M8vM8a.p.value<0.05 &
tab$bats_PValue_PamlM7M8>0.05],
tab$bats_PValue_PamlM7M8[tab$hawkins_Positive.Selection..M8vM8a.p.value<0.05 &
tab$bats_PValue_PamlM7M8>0.05], col="green", pch=20)
tab$bats_codemlM7M8.p.value>0.05],
tab$bats_codemlM7M8.p.value[tab$hawkins_Positive.Selection..M8vM8a.p.value<0.05 &
tab$bats_codemlM7M8.p.value>0.05], col="green", pch=20)
legend("topleft", c("<0.05 in DGINN-bats but >0.05 in Hawkins",
......@@ -561,7 +556,7 @@ I will draw a venn diagramm for the positive genes in the 3 analyses.
\subsubsection{subtab}
<<subbats>>=
tmp<-na.omit(tab[,c("Gene.name", "bats_PValue_PamlM7M8", "hawkins_Positive.Selection..M8vM8a.p.value", "cooper.batsM7.M8_p_value")])
tmp<-na.omit(tab[,c("Gene.name", "bats_codemlM7M8.p.value", "hawkins_Positive.Selection..M8vM8a.p.value", "cooper.batsM7.M8_p_value")])
dim(tmp)
@
......@@ -569,24 +564,43 @@ dim(tmp)
\subsubsection{figure}
<<vennbats>>=
area1dginn<-sum(tmp$bats_PValue_PamlM7M8<0.05, na.rm=T)
area1dginn<-sum(tmp$bats_codemlM7M8.p.value<0.05, na.rm=T)
area2hawk<-sum(tmp$hawkins_Positive.Selection..M8vM8a.p.value<0.05, na.rm=T)
area3coop<-sum(tmp$cooper.batsM7.M8_p_value<0.05, na.rm=T)
n12<-sum(tmp$bats_PValue_PamlM7M8<0.05 & tmp$hawkins_Positive.Selection..M8vM8a.p.value<0.05, na.rm=T)
n12<-sum(tmp$bats_codemlM7M8.p.value<0.05 & tmp$hawkins_Positive.Selection..M8vM8a.p.value<0.05, na.rm=T)
n23<-sum(tmp$hawkins_Positive.Selection..M8vM8a.p.value<0.05 & tmp$cooper.batsM7.M8_p_value<0.05, na.rm=T)
n13<-sum(tmp$bats_PValue_PamlM7M8<0.05 & tmp$cooper.batsM7.M8_p_value<0.05, na.rm=T)
n13<-sum(tmp$bats_codemlM7M8.p.value<0.05 & tmp$cooper.batsM7.M8_p_value<0.05, na.rm=T)
n123<-sum(tmp$bats_codemlM7M8.p.value<0.05 & tmp$hawkins_Positive.Selection..M8vM8a.p.value<0.05 & tmp$cooper.batsM7.M8_p_value<0.05, na.rm=T)
draw.triple.venn(area1dginn, area2hawk, area3coop,
n12, n23, n13, n123,
category=c("DGINN-Young-bats", "Hawkins-bats", "Cooper-bats"))
@
n123<-sum(tmp$bats_PValue_PamlM7M8<0.05 & tmp$hawkins_Positive.Selection..M8vM8a.p.value<0.05 & tmp$cooper.batsM7.M8_p_value<0.05, na.rm=T)
\subsection{Mondrian}
<<mondrianbats>>=
library(Mondrian)
draw.triple.venn(area1dginn, area2hawk, area3coop, n12, n23, n13, n123, category=c("dginn", "hawkins", "cooper"))
monddata<-as.data.frame(tmp$Gene.name)
monddata$bats_dginn<-ifelse(tmp$bats_codemlM7M8.p.value<0.05, 1,0)
monddata$bats_hawkins<-ifelse(tmp$hawkins_Positive.Selection..M8vM8a.p.value<0.05, 1, 0)
monddata$bats_cooper<-ifelse(tmp$cooper.batsM7.M8_p_value<0.05, 1, 0)
mondrian(monddata[,2:4])
@
\section{To do}
Comparaison G4 pas G4
\end{document}
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