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R/InterfaceqPCRtot.R
In InterfaceqPCR: GUI to Analyse qPCR Results after PMA Treatment or not
Defines functions
Interface_qPCR
#
# # \\\||||||///
# # \\ ~ ~ //
# # ( @ @ )
# # ________________oOOo-(_)-oOOo________________
# # | |
# # | Interface qPCR package |
# # | Analyse des donnees qPCR |
# # | chargement fichier gamme etalon |
# # | chargement fichier echantillons |
# # | Decembre 2016 |
# # |______________________Oooo.__________________|
# # .oooO ( )
# # ( ) ) /
# # \ ( (_/
# # \_)
# #
# # Author: Olivier Le Goff
# ###############################################################################
# ###############################################################################
Interface_qPCR <- function(){
choix_langue<-texte1<-texte2<-texte3<-texte4<-texte5<-texte6<-texte7<-texte8<-texte9<-texte10<-texte11<-texte12<-texte13<-
texte14<-texte15<-texte16<-texte17<-texte18<-texte19<-texte20<-texte21<-texte22<-texte23<-texte24<-texte25<-
texte26<-texte27<-texte28<-texte29<-texte30<-texte31<-texte32<-texte33<-texte33bis<-texte34<-texte35<-texte36<-
texte37<-texte38<-texte39<-texte40<-texte41<-texte42<-texte43<-texte44<-texte45<-texte46<-texte47<-texte48<-
texte48bis<-texte49<-texte50<-texte51<-texte52<-texte52bis<-texte53<-texte54<-texte55<-texte56<-texte57<-
texte58<-texte59<-texte60<-texte61<-texte62<-Echantillons_bruts<-choixconcentration<-Condition<-regressionnontraite<-
dataimportees_echantillons<-data_moy_ADN_nontraite<-Efficacitenontraite<-regressionnontraite<-choixconcentration<-
Ct<-dataimportees_gamme_etalon<-couleur1_ech<-couleur1<-Nbechantillons2 <-NULL
#require(tcltk)
tclRequire("BWidget")
rm(list=ls())
if(exists("dataimportees_gamme_etalon")==TRUE) {rm(dataimportees_gamme_etalon, pos=1)}
if(exists("dataimportees_echantillons")==TRUE) {rm(dataimportees_echantillons, pos=1)}
couleur1 <<- "red"
couleur1_ech <<- "red"
Nbechantillons2 <<- NA
# D\u00e9but interface graphique
Interface_Total_qPCR <- tktoplevel()
#tkwm.title(Interface_Total_qPCR,"Interface qPCR \u00e9chantillons non trait\u00e9s au PMA")
tkwm.title(Interface_Total_qPCR,texte45)
tkconfigure(Interface_Total_qPCR,bg="wheat1",cursor="hand2")
# Taille
tkwm.geometry(Interface_Total_qPCR, "700x700") # Largueur x hauteur
tkwm.resizable(Interface_Total_qPCR,F,F)
# Police
fontHeading <- tkfont.create(family="times",size=20,weight="bold",slant="italic")
font2 <- tkfont.create(family="times",size=14,weight="bold",slant="italic")
font3 <- tkfont.create(family="times",size=12,weight="bold")
## Import xlsx file
importfilexlsx_gamme_etalon <- function(){
#require(xlsx)
Total_gamme_std <- matrix(c(".xlsx",".xlsx"),1, 2, byrow = TRUE)
fil <- if(interactive()) tk_choose.files(filters = Total_gamme_std)
# Detectionchargementxlsx <- loadedNamespaces()
# if(any(Detectionchargementxlsx =="xlsx") == TRUE){dataimportees_gamme_etalon=read.xlsx(fil[1],header=T, 1)
# } else {requireNamespace(readxl)
# dataimportees_gamme_etalon <- read_excel(fil[1])
# }
dataimportees_gamme_etalon=read.xlsx(fil[1],header=T, 1)
dataimportees_gamme_etalon <<- dataimportees_gamme_etalon
dataimportees_gamme_etalon <<- dataimportees_gamme_etalon
donnees1_gamme_etalon <- dataimportees_gamme_etalon
donnees1_gamme_etalon <<- donnees1_gamme_etalon
}
## Import xlsx file
importfilexlsx_echantillons <- function(){
#require(xlsx)
Total_echnoPMA <- matrix(c(".xlsx",".xlsx"),1, 2, byrow = TRUE)
fil_ech <- if(interactive()) tk_choose.files(filters = Total_echnoPMA)
#
# Detectionchargementxlsx <- loadedNamespaces()
# if(any(Detectionchargementxlsx =="xlsx") == TRUE){dataimportees_echantillons=read.xlsx(fil_ech[1],header=T, 1)
# } else {requireNamespace(readxl)
# dataimportees_echantillons <- read_excel(fil_ech[1])
# }
dataimportees_echantillons=read.xlsx(fil_ech[1],header=T, 1)
dataimportees_echantillons <<- dataimportees_echantillons
dataimportees_echantillons <<- dataimportees_echantillons
donnees1_echantillons <- dataimportees_echantillons
donnees1_echantillons <<- donnees1_echantillons
}
###########################################################################################
## Importer le fichier des donn\u00e9es brutes
#etape1=tklabel(Interface_Total_qPCR, text="1 Importer les fichiers",font=fontHeading,foreground="chocolate4",bg="wheat1")
etape1 <- tklabel(Interface_Total_qPCR, text=texte18,font=fontHeading,foreground="chocolate4",bg="wheat1")
tkgrid(etape1, row=1, columnspan=4, sticky ="w")
## Fichier contenant la gamme \u00e9talon
#etape11=tklabel(Interface_Total_qPCR, text="Fichier Gamme \u00e9talon",font=font2,foreground="chocolate4",bg="wheat1")
etape11 <- tklabel(Interface_Total_qPCR, text=texte19,font=font2,foreground="chocolate4",bg="wheat1")
tkgrid(etape11, row=2, columnspan=4)
#import xlsx file
IMPORTxlsx.but <- tkbutton(Interface_Total_qPCR,command=importfilexlsx_gamme_etalon)
tkconfigure(IMPORTxlsx.but,image=tkimage.create("photo",file=file.path(path.package("InterfaceqPCR"),"xlsx.gif",
fsep=.Platform$file.sep)))
tkgrid(IMPORTxlsx.but,row=3,column=4)
# V\u00e9rification de l importation du fichier de donn\u00e9es brutes
Verif_import23 <- function(){
#if(exists("dataimportees_gamme_etalon")==TRUE) {"Oui"} else {"Non"}
if(exists("dataimportees_gamme_etalon")==TRUE) {texte15}else {texte16}
}
Verif_couleur <- function()
{
couleur1 <- if(exists("dataimportees_gamme_etalon")==TRUE) {"green"}else {"red"}
couleur1 <<- couleur1
}
Verif_couleur()
Verifimport2 <- Verif_import23()
#ImportationFichiertest<-tklabel(Interface_Total_qPCR, text=" Fichier cr\u00e9\u00e9 :" ,bg="wheat1")
ImportationFichiertest <- tklabel(Interface_Total_qPCR, text=texte23 ,bg="wheat1")
tkgrid(ImportationFichiertest, row=3, column=5, sticky="e")
ImportationFichiercase <- tkentry(Interface_Total_qPCR,width=10,foreground=couleur1, bg="black", textvariable=tclVar(Verifimport2))
tkgrid(ImportationFichiercase,row=3,column=6)
# Actualiser la v\u00e9rif du fichier importe
Actualisationimport <- function(){
Verif_import23 <- function(){
#if(exists("dataimportees_gamme_etalon")==TRUE) {"Oui"} else {"Non"}
if(exists("dataimportees_gamme_etalon")==TRUE) {texte15}else {texte16}
}
Verif_couleur <- function()
{
couleur1 <- if(exists("dataimportees_gamme_etalon")==TRUE) {"green"}else {"red"}
couleur1 <<- couleur1
}
Verif_couleur()
Verifimport22 <- Verif_import23()
#ImportationFichiertest<-tklabel(Interface_Total_qPCR, text=" Fichier cr\u00e9\u00e9 :" ,bg="wheat1")
ImportationFichiertest <- tklabel(Interface_Total_qPCR, text=texte23,bg="wheat1")
tkgrid(ImportationFichiertest, row=3, column=5, sticky="e")
ImportationFichiercase <- tkentry(Interface_Total_qPCR,width=10,bg="black",foreground=couleur1, textvariable=tclVar(Verifimport22))
tkgrid(ImportationFichiercase,row=3,column=6)
}
#Actualiser.but<-tkbutton(Interface_Total_qPCR,text="Actualiser", command=Actualisationimport)
Actualiser.but <- tkbutton(Interface_Total_qPCR,text=texte24, command=Actualisationimport)
tkgrid(Actualiser.but,row=3,column=7)
## Fichier contenant les echantillons
vide1 <- tklabel(Interface_Total_qPCR, text=" ",font=font2,foreground="chocolate4",bg="wheat1")
tkgrid(vide1, row=4, columnspan=4)
#etape1111=tklabel(Interface_Total_qPCR, text="Fichier Echantillons",font=font2,foreground="chocolate4",bg="wheat1")
etape1111 <- tklabel(Interface_Total_qPCR, text=texte25,font=font2,foreground="chocolate4",bg="wheat1")
tkgrid(etape1111, row=5, columnspan=4)
#import xlsx file echantillons
IMPORTxlsx_echantillons.but <- tkbutton(Interface_Total_qPCR,command=importfilexlsx_echantillons)
tkconfigure(IMPORTxlsx_echantillons.but,image=tkimage.create("photo",file=file.path(path.package("InterfaceqPCR"),"xlsx.gif",
fsep=.Platform$file.sep)))
tkgrid(IMPORTxlsx_echantillons.but,row=6,column=4)
# V\u00e9rification de l'importation du fichier de donn\u00e9es brutes
Verif_import24 <- function(){
#if(exists("dataimportees_gamme_etalon")==TRUE) {"Oui"} else {"Non"}
if(exists("dataimportees_echantillons")==TRUE) {texte15}else {texte16}
}
Verif_couleur_ech <- function()
{
couleur1_ech <- if(exists("dataimportees_echantillons")==TRUE) {"green"}else {"red"}
couleur1_ech <<- couleur1_ech
}
Verif_couleur_ech()
Verifimport_ech2 <- Verif_import24()
#ImportationFichierechantillons<-tklabel(Interface_Total_qPCR, text=" Fichier cr\u00e9\u00e9 :" ,bg="wheat1")
ImportationFichierechantillons <- tklabel(Interface_Total_qPCR, text=texte23 ,bg="wheat1")
tkgrid(ImportationFichierechantillons, row=6, column=5, sticky="e")
ImportationFichier_ech_case <- tkentry(Interface_Total_qPCR,width=10,foreground=couleur1_ech, bg="black", textvariable=tclVar(Verifimport_ech2))
tkgrid(ImportationFichier_ech_case,row=6,column=6)
# Actualiser la v\u00e9rif du fichier importe
Actualisationimport_ech <- function(){
#if(exists("dataimportees_echantillons")==TRUE) {"Oui"} else {"Non"}
if(exists("dataimportees_echantillons")==TRUE) {texte15}else {texte16}
Verif_import24 <- function(){
#if(exists("dataimportees_gamme_etalon")==TRUE) {"Oui"} else {"Non"}
if(exists("dataimportees_echantillons")==TRUE) {texte15}else {texte16}
}
Verif_couleur_ech <- function()
{
couleur1_ech <- if(exists("dataimportees_echantillons")==TRUE) {"green"}else {"red"}
couleur1_ech <<- couleur1_ech
}
Verif_couleur_ech()
Verifimport_ech22 <- Verif_import24()
#ImportationFichierechantillons<-tklabel(Interface_Total_qPCR, text=" Fichier cr\u00e9\u00e9 :" ,bg="wheat1")
ImportationFichierechantillons <- tklabel(Interface_Total_qPCR, text=texte23 ,bg="wheat1")
tkgrid(ImportationFichierechantillons, row=6, column=5, sticky="e")
ImportationFichier_ech_case <- tkentry(Interface_Total_qPCR,width=10, foreground=couleur1_ech, bg="black", textvariable=tclVar(Verifimport_ech22))
tkgrid(ImportationFichier_ech_case,row=6,column=6)
###
Calcul_Nb_echantillons2 = function(){
if(exists("dataimportees_echantillons")==FALSE) {" "}else{
Nbechantillons <- subset(dataimportees_echantillons, ! Condition %in% c("PMA"))
Nbechantillons2 <- length(Nbechantillons$Nom_Echantillon)
Nbechantillons2 <<- Nbechantillons2
}
}
Calcul_Nb_echantillons = function(){
if(exists("dataimportees_echantillons")==FALSE) {" "} else {Calcul_Nb_echantillons2()}
}
ImportationNbFichier_ech_case <- tkentry(Interface_Total_qPCR,width=10,foreground=couleur1_ech,
font=font3, bg="black",
textvariable=tclVar(Calcul_Nb_echantillons()))
tkgrid(ImportationNbFichier_ech_case,row=14,column=3)
}
#Actualiserech.but<-tkbutton(Interface_Total_qPCR,text="Actualiser", command=Actualisationimport_ech)
Actualiserech.but <- tkbutton(Interface_Total_qPCR,text=texte24, command=Actualisationimport_ech)
tkgrid(Actualiserech.but,row=6,column=7)
##################################################################################################
## Importer le fichier des donn\u00e9es brutes
vide2 <- tklabel(Interface_Total_qPCR, text="",font=fontHeading,foreground="chocolate4",bg="wheat1")
tkgrid(vide2, row=7, columnspan=4)
#etape2=tklabel(Interface_Total_qPCR, text="2 Droite de r\u00e9gression",font=fontHeading,foreground="chocolate4",bg="wheat1")
etape2 <- tklabel(Interface_Total_qPCR, text=texte27,font=fontHeading,foreground="chocolate4",bg="wheat1")
tkgrid(etape2, row=8, columnspan=4, sticky="w")
## Ajout du choix de la concentration
#etape21=tklabel(Interface_Total_qPCR, text="Concentration en :",font=font2,foreground="chocolate4",bg="wheat1")
etape21 <- tklabel(Interface_Total_qPCR, text=texte51,font=font2,foreground="chocolate4",bg="wheat1")
tkgrid(etape21, row=9, column=2)
# radio boutons
rb1_UFC <- tkradiobutton(Interface_Total_qPCR, font=font3,foreground="black",bg="wheat1")
rb2_copies <- tkradiobutton(Interface_Total_qPCR, font=font3,foreground="black",bg="wheat1")
# Choix par d\u00e9faut
rbValue <- tclVar(texte52)
# config des boutons radio. Une seule variable tcl pour 2 boutons
#tkconfigure(rb2_copies,variable=rbValue,value=" UFC/mL", text=" UFC/mL")
tkconfigure(rb1_UFC,variable=rbValue,value=texte52, text=texte52)
#tkconfigure(rb2_copies,variable=rbValue,value="Nb copies/mL", text="Nb copies/mL")
tkconfigure(rb2_copies,variable=rbValue,value=texte53, text=texte53)
tkgrid(rb1_UFC,row=9, column=3)
tkgrid(rb2_copies,row=9,column=5)
#etape212=tklabel(Interface_Total_qPCR, text="ou",font=font3,foreground="chocolate4",bg="wheat1")
etape212=tklabel(Interface_Total_qPCR, text=texte22,font=font3,foreground="chocolate4",bg="wheat1")
tkgrid(etape212,row=9,column=4)
OnOK <- function() {
#message<-paste("Votre choix est :", tclvalue(rbValue))
message<-paste(texte54, tclvalue(rbValue))
tkmessageBox(title="Validation", message=message, icon="info", type="ok")
choixconcentration <<-tclvalue(rbValue)
}
OK.but <- tkbutton(Interface_Total_qPCR, text="OK", command=OnOK)
tkgrid(OK.but,row=9,column=6)
# Calcul et tracage de droite de regression issue des standards
Calcul_regression <- function(){
#library(reshape2)
#library(plyr)
fusion_data <- dataimportees_gamme_etalon
head(fusion_data)
# Calculer moyenne et ecart type par Standard
data_moy_sd <- ddply(fusion_data,c("Numero","Standard","log10_Sdt","Condition"),summarise,
Moy=mean(Ct,na.rm=TRUE),
sd=sd(Ct,na.rm=TRUE))
data_moy_sd
data_moy_sd <<- data_moy_sd[complete.cases(data_moy_sd), ]
# equation de la droite de regression ADN non traite issue de data_moy_sd
data_moy_ADN_nontraite <- subset(data_moy_sd, Condition=="Total")
data_moy_ADN_nontraite <<- data_moy_ADN_nontraite
regressionnontraite <- lm(data_moy_ADN_nontraite$Moy~data_moy_ADN_nontraite$log10_Sdt,data_moy_ADN_nontraite)
regressionnontraite <<- regressionnontraite
pentenontraite <- format(regressionnontraite$coefficients[2], digits = 3)
interceptionnontraite <- format(regressionnontraite$coefficients[1], digits = 4)
r2nontraite <- format(summary(regressionnontraite)$r.squared, digits = 3)
r2nontraite <<- r2nontraite
Efficacitenontraite <- format((-1+(10^(-1/summary(regressionnontraite)$coefficients[2])))*100, digits = 3)
if(Efficacitenontraite>100){Efficacitenontraite=100}else{Efficacitenontraite}
Efficacitenontraite <<- Efficacitenontraite
equation_droitenontraite <- paste("y =",interceptionnontraite , pentenontraite ,"x" )
R2equation_droitenontraite <- paste("R2 =", r2nontraite)
Efficaciteequation_droitenontraite <- paste("E =", Efficacitenontraite,"%")
equation_droitenontraite <<- equation_droitenontraite
R2equation_droitenontraite <<- R2equation_droitenontraite
Efficaciteequation_droitenontraite <<- Efficaciteequation_droitenontraite
}
graphique_regression <- function(){
#library(tkrplot)
fenetre_graphique <- tktoplevel()
#tkwm.title(fenetre_graphique,"Droite de regression issue des Standards qPCR")
tkwm.title(fenetre_graphique, texte28)
tkconfigure(fenetre_graphique,bg="wheat1",cursor="hand2")
# Taille
tkwm.geometry(fenetre_graphique, "625x700") # Largueur x hauteur
tkwm.resizable(fenetre_graphique,F,F)
image1plot <- function(){
#
# Condition si concentration en UFC/mL
if(choixconcentration == texte52) {
###########
XX <- log10(data_moy_ADN_nontraite$Standard)
#XX<-data_moy_ADN_nontraite$Standard
YY <- data_moy_ADN_nontraite$Moy
REGRESSION_PENTE <- format(regressionnontraite$coefficients[2], digits = 3)
REGRESSION_INTERCEPTION <- format(regressionnontraite$coefficients[1], digits = 3)
r2STD <- format(summary(regressionnontraite)$r.squared, digits = 3)
Efficacitetrace <- Efficacitenontraite
LODtracetraite <- ceiling(10^(3*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
LOQtracetraite <- ceiling(10^(10*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
par(lab=c(10,10,10),oma=c(5,2,0,0))
plot(XX,YY,cex.axis=0.7,las=1,xlim=c(0,10),ylim=c(0,50),
pch=16,col="red",
main="",
xlab=" ",
ylab=expression(paste(C[t], "value")))
#abline(lm(data_moy_ADN_nontraite$Moy~data_moy_ADN_nontraite$log10_Sdt,data_moy_ADN_nontraite))
#ecarts-types mis sur le barplot
arrows(XX, data_moy_ADN_nontraite$Moy + data_moy_ADN_nontraite$sd,
XX, data_moy_ADN_nontraite$Moy - data_moy_ADN_nontraite$sd,
length = 0.05, # width of the arrowhead
angle = 90,
code = 3)
abline(b = REGRESSION_PENTE, a = REGRESSION_INTERCEPTION,col="black")
legend("topright",legend=paste("y =", REGRESSION_PENTE ,"x + ",REGRESSION_INTERCEPTION, "\nR2 =", r2STD,
"\nE=",Efficacitetrace, " %",
"\nLOD=",LODtracetraite, texte52,
"\nLOQ=",LOQtracetraite, texte52),bty="n",cex=0.75)
axis(1,at=c(0,sort(XX)),labels=format(c(0,sort(data_moy_ADN_nontraite$Standard)),scientific=TRUE,digits = 3),
line=3,col="blue",col.ticks="blue",col.axis="blue",cex.axis=0.75, las=2)
# text(-1,-10,"UFC/mL", cex= 0.8,col="blue",xpd=TRUE)
text(-1,-10, texte52 , cex= 0.8,col="blue",xpd=TRUE)
#text(-1,-6,expression(paste(Log[10],"(UFC/mL)")), cex= 0.7,col="black",xpd=TRUE)
text(-1,-6, texte52bis , cex= 0.7,col="black",xpd=TRUE)
#
#
# si condition concentration est Nb copies/mL
}else{
###########
XX <- log10(data_moy_ADN_nontraite$Standard)
#XX<-data_moy_ADN_nontraite$Standard
YY <- data_moy_ADN_nontraite$Moy
REGRESSION_PENTE <- format(regressionnontraite$coefficients[2], digits = 3)
REGRESSION_INTERCEPTION <- format(regressionnontraite$coefficients[1], digits = 3)
r2STD <- format(summary(regressionnontraite)$r.squared, digits = 3)
Efficacitetrace <- Efficacitenontraite
LODtracetraite <- ceiling(10^(3*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
LOQtracetraite <- ceiling(10^(10*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
par(lab=c(10,10,10),oma=c(5,2,0,0))
plot(XX,YY,cex.axis=0.7,las=1,xlim=c(0,10),ylim=c(0,50),
pch=16,col="red",
main="",
xlab=" ",
ylab=expression(paste(C[t], "value")))
#abline(lm(data_moy_ADN_nontraite$Moy~data_moy_ADN_nontraite$log10_Sdt,data_moy_ADN_nontraite))
#ecarts-types mis sur le barplot
arrows(XX, data_moy_ADN_nontraite$Moy + data_moy_ADN_nontraite$sd,
XX, data_moy_ADN_nontraite$Moy - data_moy_ADN_nontraite$sd,
length = 0.05, # width of the arrowhead
angle = 90,
code = 3)
abline(b = REGRESSION_PENTE, a = REGRESSION_INTERCEPTION,col="black")
legend("topright",legend=paste("y =", REGRESSION_PENTE ,"x + ",REGRESSION_INTERCEPTION, "\nR2 =", r2STD,
"\nE=",Efficacitetrace, " %",
"\nLOD=",LODtracetraite, "copies/mL",
"\nLOQ=",LOQtracetraite, "copies/mL"),bty="n",cex=0.75)
axis(1,at=c(0,sort(XX)),labels=format(c(0,sort(data_moy_ADN_nontraite$Standard)),scientific=TRUE,digits=3),
line=3,col="blue",col.ticks="blue",col.axis="blue",cex.axis=0.75, las=2)
text(-1,-10,"copies/mL", cex= 0.8,col="blue",xpd=TRUE)
text(-1,-6,expression(paste(Log[10], " (copies/mL)")), cex= 0.7,col="black",xpd=TRUE)
}
} # fin fonction image1
image1 <- tkrplot(fenetre_graphique,fun=image1plot,hscale=1.9,vscale=1.9)
tkgrid(image1,columnspan=5,rowspan=4)
exportertiffplot <- function() {
# Exportationfichiertiff1=tkmessageBox(title="Enregistrer en .tiff", message="Voulez-vous enregistrer en .tiff ?",
# icon="info",type="yesno")
Exportationfichiertiff1=tkmessageBox(title=texte55, message=texte56 ,
icon="info",type="yesno")
Exportationfichiertiff11<-tclvalue(Exportationfichiertiff1)
if(Exportationfichiertiff11=="yes" & choixconcentration ==texte52) {
XX <- log10(data_moy_ADN_nontraite$Standard)
#XX<-data_moy_ADN_nontraite$Standard
YY <- data_moy_ADN_nontraite$Moy
REGRESSION_PENTE <- format(regressionnontraite$coefficients[2], digits = 3)
REGRESSION_INTERCEPTION <- format(regressionnontraite$coefficients[1], digits = 3)
r2STD <- format(summary(regressionnontraite)$r.squared, digits = 3)
Efficacitetrace <- Efficacitenontraite
LODtracetraite <- ceiling(10^(3*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
LOQtracetraite <- ceiling(10^(10*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
FigureExportee_Tiff <- tclvalue(tkgetSaveFile())
figureExportee_Tiff <- paste(FigureExportee_Tiff,".tiff",sep="")
Standard_curves_UFC_mL <- function() {
par(lab=c(10,10,10),oma=c(5,2,0,0))
plot(XX,YY,cex.axis=0.7,las=1,xlim=c(0,10),ylim=c(0,50),
pch=16,col="red",
main="",
xlab=" ",
ylab=expression(paste(C[t], "value")))
#abline(lm(data_moy_ADN_nontraite$Moy~data_moy_ADN_nontraite$log10_Sdt,data_moy_ADN_nontraite))
arrows(XX, data_moy_ADN_nontraite$Moy + data_moy_ADN_nontraite$sd,
XX, data_moy_ADN_nontraite$Moy - data_moy_ADN_nontraite$sd,
length = 0.05, # width of the arrowhead
angle = 90,
code = 3)
abline(b = REGRESSION_PENTE, a = REGRESSION_INTERCEPTION,col="black")
legend("topright",legend=paste("y =", REGRESSION_PENTE ,"x + ",REGRESSION_INTERCEPTION, "\nR2 =", r2STD,
"\nE=",Efficacitetrace, " %",
"\nLOD=",LODtracetraite, texte52,
"\nLOQ=",LOQtracetraite, texte52),bty="n",cex=0.75)
axis(1,at=c(0,sort(XX)),labels=format(c(0,sort(data_moy_ADN_nontraite$Standard)),scientific=TRUE,digits = 3),
line=3,col="blue",col.ticks="blue",col.axis="blue",cex.axis=0.75, las=2)
# text(-1,-10,"UFC/mL", cex= 0.8,col="blue",xpd=TRUE)
text(-1,-10, texte52 , cex= 0.8,col="blue",xpd=TRUE)
#text(-1,-6,expression(paste(Log[10],"(UFC/mL)")), cex= 0.7,col="black",xpd=TRUE)
text(-1,-6, texte52bis, cex= 0.7,col="black",xpd=TRUE)
}
tiff(filename=figureExportee_Tiff, compression = "lzw",
height=18, width=18, units="cm", res=400)
Standard_curves_UFC_mL()
dev.off()
}else{
if(Exportationfichiertiff11=="yes" & choixconcentration == texte53){
XX <- log10(data_moy_ADN_nontraite$Standard)
#XX<-data_moy_ADN_nontraite$Standard
YY <- data_moy_ADN_nontraite$Moy
REGRESSION_PENTE <- format(regressionnontraite$coefficients[2], digits = 3)
REGRESSION_INTERCEPTION <- format(regressionnontraite$coefficients[1], digits = 3)
r2STD <- format(summary(regressionnontraite)$r.squared, digits = 3)
Efficacitetrace <- Efficacitenontraite
LODtracetraite <- ceiling(10^(3*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
LOQtracetraite <- ceiling(10^(10*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
FigureExportee_Tiff <- tclvalue(tkgetSaveFile())
figureExportee_Tiff <- paste(FigureExportee_Tiff,".tiff",sep="")
Standard_curves_copies_mL <- function() {
par(lab=c(10,10,10),oma=c(5,2,0,0))
plot(XX,YY,cex.axis=0.7,las=1,xlim=c(0,10),ylim=c(0,50),
pch=16,col="red",
main="",
xlab="",
ylab=expression(paste(C[t], "value")))
#abline(lm(data_moy_ADN_nontraite$Moy~data_moy_ADN_nontraite$log10_Sdt,data_moy_ADN_nontraite))
arrows(XX, data_moy_ADN_nontraite$Moy + data_moy_ADN_nontraite$sd,
XX, data_moy_ADN_nontraite$Moy - data_moy_ADN_nontraite$sd,
length = 0.05, # width of the arrowhead
angle = 90,
code = 3)
abline(b = REGRESSION_PENTE, a = REGRESSION_INTERCEPTION,col="black")
legend("topright",legend=paste("y =", REGRESSION_PENTE ,"x + ",REGRESSION_INTERCEPTION, "\nR2 =", r2STD,
"\nE=",Efficacitetrace, " %",
"\nLOD=",LODtracetraite, "copies/mL",
"\nLOQ=",LOQtracetraite, "copies/mL"),bty="n",cex=0.75)
axis(1,at=c(0,sort(XX)),labels=format(c(0,sort(data_moy_ADN_nontraite$Standard)),scientific=TRUE,digits=3),
line=3,col="blue",col.ticks="blue",col.axis="blue",cex.axis=0.75, las=2)
text(-1,-10,"copies/mL", cex= 0.8,col="blue",xpd=TRUE)
text(-1,-6,expression(paste(Log[10], " (copies/mL)")), cex= 0.7,col="black",xpd=TRUE)
}
tiff(filename=figureExportee_Tiff, compression = "lzw",
height=18, width=18, units="cm", res=400)
Standard_curves_copies_mL()
dev.off()
}else{}
}
}
Export_Tiff.but <- tkbutton(fenetre_graphique, command=exportertiffplot)
tkconfigure(Export_Tiff.but,image=tkimage.create("photo",file=file.path(path.package("InterfaceqPCR"),"tiff.gif",
fsep=.Platform$file.sep)))
tkgrid(Export_Tiff.but, row=4, column=0)
exporterjpegplot <- function() {
Exportationfichierjpeg1=tkmessageBox(title= texte57, message= texte58,
icon="info",type="yesno")
Exportationfichierjpeg11<-tclvalue(Exportationfichierjpeg1)
if(Exportationfichierjpeg11=="yes" & choixconcentration == texte52) {
XX <- log10(data_moy_ADN_nontraite$Standard)
#XX<-data_moy_ADN_nontraite$Standard
YY <- data_moy_ADN_nontraite$Moy
REGRESSION_PENTE <- format(regressionnontraite$coefficients[2], digits = 3)
REGRESSION_INTERCEPTION <- format(regressionnontraite$coefficients[1], digits = 3)
r2STD <- format(summary(regressionnontraite)$r.squared, digits = 3)
Efficacitetrace <- Efficacitenontraite
LODtracetraite <- ceiling(10^(3*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
LOQtracetraite <- ceiling(10^(10*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
FigureExportee_Jpeg <- tclvalue(tkgetSaveFile())
figureExportee_Jpeg <- paste(FigureExportee_Jpeg,".jpeg",sep="")
Standard_curves_UFC_mL <- function() {
par(lab=c(10,10,10),oma=c(5,2,0,0))
plot(XX,YY,cex.axis=0.7,las=1,xlim=c(0,10),ylim=c(0,50),
pch=16,col="red",
main="",
xlab=" ",
ylab=expression(paste(C[t], "value")))
#abline(lm(data_moy_ADN_nontraite$Moy~data_moy_ADN_nontraite$log10_Sdt,data_moy_ADN_nontraite))
arrows(XX, data_moy_ADN_nontraite$Moy + data_moy_ADN_nontraite$sd,
XX, data_moy_ADN_nontraite$Moy - data_moy_ADN_nontraite$sd,
length = 0.05, # width of the arrowhead
angle = 90,
code = 3)
abline(b = REGRESSION_PENTE, a = REGRESSION_INTERCEPTION,col="black")
legend("topright",legend=paste("y =", REGRESSION_PENTE ,"x + ",REGRESSION_INTERCEPTION, "\nR2 =", r2STD,
"\nE=",Efficacitetrace, " %",
"\nLOD=",LODtracetraite, texte52,
"\nLOQ=",LOQtracetraite, texte52),bty="n",cex=0.75)
axis(1,at=c(0,sort(XX)),labels=format(c(0,sort(data_moy_ADN_nontraite$Standard)),scientific=TRUE,digits = 3),
line=3,col="blue",col.ticks="blue",col.axis="blue",cex.axis=0.75, las=2)
# text(-1,-10,"UFC/mL", cex= 0.8,col="blue",xpd=TRUE)
text(-1,-10, texte52, cex= 0.8,col="blue",xpd=TRUE)
#text(-1,-6,expression(paste(Log[10],"(UFC/mL)")), cex= 0.7,col="black",xpd=TRUE)
text(-1,-6, texte52bis , cex= 0.7,col="black",xpd=TRUE)
}
jpeg(filename=figureExportee_Jpeg, height=18, width=18, units="cm", res=400)
Standard_curves_UFC_mL()
dev.off()
}else{
if(Exportationfichierjpeg11=="yes" & choixconcentration == texte53){
XX <- log10(data_moy_ADN_nontraite$Standard)
#XX<-data_moy_ADN_nontraite$Standard
YY <- data_moy_ADN_nontraite$Moy
REGRESSION_PENTE <- format(regressionnontraite$coefficients[2], digits = 3)
REGRESSION_INTERCEPTION <- format(regressionnontraite$coefficients[1], digits = 3)
r2STD <- format(summary(regressionnontraite)$r.squared, digits = 3)
Efficacitetrace <- Efficacitenontraite
LODtracetraite <- ceiling(10^(3*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
LOQtracetraite <- ceiling(10^(10*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
FigureExportee_Jpeg <- tclvalue(tkgetSaveFile())
figureExportee_Jpeg <- paste(FigureExportee_Jpeg,".jpeg",sep="")
Standard_curves_copies_mL <- function() {
par(lab=c(10,10,10),oma=c(5,2,0,0))
plot(XX,YY,cex.axis=0.7,las=1,xlim=c(0,10),ylim=c(0,50),
pch=16,col="red",
main="",
xlab="",
ylab=expression(paste(C[t], "value")))
#abline(lm(data_moy_ADN_nontraite$Moy~data_moy_ADN_nontraite$log10_Sdt,data_moy_ADN_nontraite))
arrows(XX, data_moy_ADN_nontraite$Moy + data_moy_ADN_nontraite$sd,
XX, data_moy_ADN_nontraite$Moy - data_moy_ADN_nontraite$sd,
length = 0.05, # width of the arrowhead
angle = 90,
code = 3)
abline(b = REGRESSION_PENTE, a = REGRESSION_INTERCEPTION,col="black")
legend("topright",legend=paste("y =", REGRESSION_PENTE ,"x + ",REGRESSION_INTERCEPTION, "\nR2 =", r2STD,
"\nE=",Efficacitetrace, " %",
"\nLOD=",LODtracetraite, "copies/mL",
"\nLOQ=",LOQtracetraite, "copies/mL"),bty="n",cex=0.75)
axis(1,at=c(0,sort(XX)),labels=format(c(0,sort(data_moy_ADN_nontraite$Standard)),scientific=TRUE,digits=3),
line=3,col="blue",col.ticks="blue",col.axis="blue",cex.axis=0.75, las=2)
text(-1,-10,"copies/mL", cex= 0.8,col="blue",xpd=TRUE)
text(-1,-6,expression(paste(Log[10], " (copies/mL)")), cex= 0.7,col="black",xpd=TRUE)
}
jpeg(filename=figureExportee_Jpeg, height=18, width=18, units="cm", res=400)
Standard_curves_copies_mL()
dev.off()
}else{}
}
}
Export_jpeg.but <- tkbutton(fenetre_graphique, command=exporterjpegplot)
tkconfigure(Export_jpeg.but,image=tkimage.create("photo",file=file.path(path.package("InterfaceqPCR"),"jpg.gif",
fsep=.Platform$file.sep)))
tkgrid(Export_jpeg.but, row=4, column=1)
exporterpdfplot <- function() {
Exportationfichierpdf1=tkmessageBox(title= texte59, message= texte60,
icon="info",type="yesno")
Exportationfichierpdf11<-tclvalue(Exportationfichierpdf1)
if(Exportationfichierpdf11=="yes" & choixconcentration == texte52) {
XX <- log10(data_moy_ADN_nontraite$Standard)
#XX<-data_moy_ADN_nontraite$Standard
YY <- data_moy_ADN_nontraite$Moy
REGRESSION_PENTE <- format(regressionnontraite$coefficients[2], digits = 3)
REGRESSION_INTERCEPTION <- format(regressionnontraite$coefficients[1], digits = 3)
r2STD <- format(summary(regressionnontraite)$r.squared, digits = 3)
Efficacitetrace <- Efficacitenontraite
LODtracetraite <- ceiling(10^(3*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
LOQtracetraite <- ceiling(10^(10*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
FigureExportee_Pdf <- tclvalue(tkgetSaveFile())
figureExportee_Pdf <- paste(FigureExportee_Pdf,".pdf",sep="")
Standard_curves_UFC_mL <- function() {
par(lab=c(10,10,10),oma=c(5,2,0,0))
plot(XX,YY,cex.axis=0.7,las=1,xlim=c(0,10),ylim=c(0,50),
pch=16,col="red",
main="",
xlab=" ",
ylab=expression(paste(C[t], "value")))
#abline(lm(data_moy_ADN_nontraite$Moy~data_moy_ADN_nontraite$log10_Sdt,data_moy_ADN_nontraite))
arrows(XX, data_moy_ADN_nontraite$Moy + data_moy_ADN_nontraite$sd,
XX, data_moy_ADN_nontraite$Moy - data_moy_ADN_nontraite$sd,
length = 0.05, # width of the arrowhead
angle = 90,
code = 3)
abline(b = REGRESSION_PENTE, a = REGRESSION_INTERCEPTION,col="black")
legend("topright",legend=paste("y =", REGRESSION_PENTE ,"x + ",REGRESSION_INTERCEPTION, "\nR2 =", r2STD,
"\nE=",Efficacitetrace, " %",
"\nLOD=",LODtracetraite, texte52,
"\nLOQ=",LOQtracetraite, texte52),bty="n",cex=0.75)
axis(1,at=c(0,sort(XX)),labels=format(c(0,sort(data_moy_ADN_nontraite$Standard)),scientific=TRUE,digits = 3),
line=3,col="blue",col.ticks="blue",col.axis="blue",cex.axis=0.75, las=2)
# text(-1,-10,"UFC/mL", cex= 0.8,col="blue",xpd=TRUE)
text(-1,-10, texte52 , cex= 0.8,col="blue",xpd=TRUE)
#text(-1,-6,expression(paste(Log[10],"(UFC/mL)")), cex= 0.7,col="black",xpd=TRUE)
text(-1,-6, texte52bis , cex= 0.7,col="black",xpd=TRUE)
}
pdf(file=figureExportee_Pdf, paper="a4r", height=9, width=9)
Standard_curves_UFC_mL()
dev.off()
}else{
if(Exportationfichierpdf11=="yes" & choixconcentration ==texte53){
XX <- log10(data_moy_ADN_nontraite$Standard)
#XX<-data_moy_ADN_nontraite$Standard
YY <- data_moy_ADN_nontraite$Moy
REGRESSION_PENTE <- format(regressionnontraite$coefficients[2], digits = 3)
REGRESSION_INTERCEPTION <- format(regressionnontraite$coefficients[1], digits = 3)
r2STD <- format(summary(regressionnontraite)$r.squared, digits = 3)
Efficacitetrace <- Efficacitenontraite
LODtracetraite <- ceiling(10^(3*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
LOQtracetraite <- ceiling(10^(10*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
FigureExportee_Pdf <- tclvalue(tkgetSaveFile())
figureExportee_Pdf <- paste(FigureExportee_Pdf,".pdf",sep="")
Standard_curves_copies_mL <- function() {
par(lab=c(10,10,10),oma=c(5,2,0,0))
plot(XX,YY,cex.axis=0.7,las=1,xlim=c(0,10),ylim=c(0,50),
pch=16,col="red",
main="",
xlab="",
ylab=expression(paste(C[t], "value")))
#abline(lm(data_moy_ADN_nontraite$Moy~data_moy_ADN_nontraite$log10_Sdt,data_moy_ADN_nontraite))
arrows(XX, data_moy_ADN_nontraite$Moy + data_moy_ADN_nontraite$sd,
XX, data_moy_ADN_nontraite$Moy - data_moy_ADN_nontraite$sd,
length = 0.05, # width of the arrowhead
angle = 90,
code = 3)
abline(b = REGRESSION_PENTE, a = REGRESSION_INTERCEPTION,col="black")
legend("topright",legend=paste("y =", REGRESSION_PENTE ,"x + ",REGRESSION_INTERCEPTION, "\nR2 =", r2STD,
"\nE=",Efficacitetrace, " %",
"\nLOD=",LODtracetraite, "copies/mL",
"\nLOQ=",LOQtracetraite, "copies/mL"),bty="n",cex=0.75)
axis(1,at=c(0,sort(XX)),labels=format(c(0,sort(data_moy_ADN_nontraite$Standard)),scientific=TRUE,digits=3),
line=3,col="blue",col.ticks="blue",col.axis="blue",cex.axis=0.75, las=2)
text(-1,-10,"copies/mL", cex= 0.8,col="blue",xpd=TRUE)
text(-1,-6, texte52bis , cex= 0.7,col="black",xpd=TRUE)
}
pdf(file=figureExportee_Pdf, paper="a4r", height=9, width=8.5)
Standard_curves_copies_mL()
dev.off()
}else{}
}
}
Export_pdf.but <- tkbutton(fenetre_graphique, command=exporterpdfplot)
tkconfigure(Export_pdf.but,image=tkimage.create("photo",file=file.path(path.package("InterfaceqPCR"),"pdf.gif",
fsep=.Platform$file.sep)))
tkgrid(Export_pdf.but, row=4, column=2)
}
videregression <- tklabel(Interface_Total_qPCR, text=" ",font=fontHeading,foreground="chocolate4",bg="wheat1")
tkgrid(videregression, row=10, columnspan=4)
Calcul_regression.but <- tkbutton(Interface_Total_qPCR,command=Calcul_regression)
tkconfigure(Calcul_regression.but,image=tkimage.create("photo",file=file.path(path.package("InterfaceqPCR"),"calcul.gif",
fsep=.Platform$file.sep)))
tkgrid(Calcul_regression.but,row=11,column=2)
graphique_regression.but <- tkbutton(Interface_Total_qPCR,command=graphique_regression)
tkconfigure(graphique_regression.but,image=tkimage.create("photo",file=file.path(path.package("InterfaceqPCR"),"Plot.gif",
fsep=.Platform$file.sep)))
tkgrid(graphique_regression.but,row=11,column=3)
##############################################################################################
###############
vide3 <- tklabel(Interface_Total_qPCR, text="",font=fontHeading,foreground="chocolate4",bg="wheat1")
tkgrid(vide3, row=12, columnspan=4)
#etape3=tklabel(Interface_Total_qPCR, text="3 Concentration dans les \u00e9chantillons",font=fontHeading,foreground="chocolate4",bg="wheat1")
etape3 <- tklabel(Interface_Total_qPCR, text=texte29,font=fontHeading,foreground="chocolate4",bg="wheat1")
tkgrid(etape3, row=13, columnspan=6, sticky ="w")
#etape31=tklabel(Interface_Total_qPCR, text="Nb \u00e9chantillons",font=font2,foreground="chocolate4",bg="wheat1")
etape31 <- tklabel(Interface_Total_qPCR, text=texte61, font=font2,foreground="chocolate4",bg="wheat1")
tkgrid(etape31, row=14, column=2)
Calcul_Nb_echantillons =function(){
if(exists("dataimportees_echantillons")==FALSE) {" "} else {
Calcul_Nb_echantillons2=function(){
Nbechantillons <- subset(dataimportees_echantillons, ! Condition %in% c("PMA"))
Nbechantillons2 <- length(Nbechantillons$Nom_Echantillon)
Nbechantillons2 <<- as.character(Nbechantillons2)
}
}
}
ImportationNbFichier_ech_case <- tkentry(Interface_Total_qPCR,width=10,foreground=couleur1_ech,
bg="black", textvariable=tclVar(Calcul_Nb_echantillons()))
tkgrid(ImportationNbFichier_ech_case,row=14,column=3)
# R\u00e9cup\u00e9ration de l'\u00e9quation pour calculer les nombres de copies des \u00e9chantillons
## ATTENTION DONNEES EN LOG 10 PENSEZ A CONVERTIR
## La formule qui suit corrige le log10
calcul_echantillons <- function(){
regequation <- data.frame(summary(regressionnontraite)$coef[,1])
#row.names(regequation)=c("interception","pente")
row.names(regequation) <- c(texte30,texte31)
#colnames(regequation)=c("Valeurs")
colnames(regequation) <- c(texte32)
regequation <<- regequation
# R\u00e9cup\u00e9ration des Echantillons et Ct
# Subset garde uniquement les donn\u00e9es non traite au PMA
dataimportees_echantillons_nontraite <- subset(dataimportees_echantillons, ! Condition %in% c("PMA"))
Echantillons_bruts <- dataimportees_echantillons_nontraite
# Selection analyse UFC/mL ou nb copies/mL
# Condition permettant de v\u00e9rifier si la colonne Concentration UFC/mL existe
# Comme elle n'existe pas, elle se cr\u00e9\u00e9e
# Condition si anglais renomme les header colonnes
if(choixconcentration == texte52 ) {
if(exists("dataimportees_echantillons$Concentration_UFC_mL")==FALSE) {dataimportees_echantillons$Concentration_UFC_mL=0} else {dataimportees_echantillons$Concentration_UFC_mL}
Echantillons_bruts <<- Echantillons_bruts
Echantillons_bruts$Concentration_UFC_mL <- 10^((Echantillons_bruts$Ct-regequation[1,])/regequation[2,])
Echantillons_bruts <<- Echantillons_bruts
}else{
if(exists("dataimportees_echantillons$Concentration_copies_mL")==FALSE) {dataimportees_echantillons$Concentration_copies_mL=0} else {dataimportees_echantillons$Concentration_copies_mL}
Echantillons_bruts <<- Echantillons_bruts
Echantillons_bruts$Concentration_copies_mL <- 10^((Echantillons_bruts$Ct-regequation[1,])/regequation[2,])
Echantillons_bruts <<- Echantillons_bruts
}
# langue selectionnee : anglais
#if(choix_langue2 == "ANGLAIS" & choixconcentration == texte52) {
if(choix_langue == "ANGLAIS" & choixconcentration == texte52) {
names(Echantillons_bruts)[1] <- "Name_Sample"
names(Echantillons_bruts)[4] <- "Concentration_CFU_mL"
Echantillons_bruts <<- Echantillons_bruts
}else{}
#if(choix_langue2 == "ANGLAIS" & choixconcentration == texte53) {
if(choix_langue == "ANGLAIS" & choixconcentration == texte53) {
names(Echantillons_bruts)[1] <- "Name_Sample"
Echantillons_bruts <<- Echantillons_bruts
}else{}
}
Tableau_Echantillons_concentration <- function(){
## covert a data frame into a character based on
.toCharacter <- function(x,width,...) UseMethod(".toCharacter")
.toCharacter.default <- function(x,width,...) as.character(x)
.toCharacter.integer <- function(x,width,...) {
if(missing(width)) width <- max(nchar(as.character(x))) + 2
format(x, justify = "right", width = width)
}
.toCharacter.numeric <- function(x,width,...) {
if(missing(width)) width <- max(nchar(as.character(x))) + 2
format(x,trim = FALSE, width = width, justify = "right")
}
.toCharacter.factor <- function(x,width,...) {
if(missing(width)) width <- max(nchar(as.character(x))) + 2
.toCharacter(as.character(x),width,...)
}
.toCharacter.logical <- function(x,width,...) {
if(missing(width)) width <- 7
format(as.character(x), justify = "centre", width = width)
}
.toCharacter.data.frame <- function(x,width = 10, ...) {
nms <- dimnames(x)
DF <- as.data.frame(lapply(x,function(i) .toCharacter(i, width = width)),
stringsAsFactors = FALSE)
dimnames(DF) <- nms
return(DF)
}
addScrollbars <- function(parent, widget) {
xscr <- ttkscrollbar(parent, orient = "horizontal",
command = function(...) tkxview(widget, ...))
yscr <- ttkscrollbar(parent, orient = "vertical",
command = function(...) tkyview(widget, ...))
tkconfigure(widget,
xscrollcommand = function(...) tkset(xscr,...),
yscrollcommand = function(...) tkset(yscr,...))
tkgrid(widget, row = 0, column = 0, sticky = "news")
tkgrid(yscr,row = 0,column = 1, sticky = "ns")
tkgrid(xscr, row = 1, column = 0, sticky = "ew")
tkgrid.columnconfigure(parent, 0, weight = 1)
tkgrid.rowconfigure(parent, 0, weight = 1)
}
affichage_concentration_Echantillons <<- Echantillons_bruts
affichage_concentration_Echantillons[,1] <- as.character(Echantillons_bruts[,1])
affichage_concentration_Echantillons[,2] <- as.character(Echantillons_bruts[,2])
affichage_concentration_Echantillons[,3] <- as.numeric(Echantillons_bruts[,3])
affichage_concentration_Echantillons[,4] <- as.numeric(Echantillons_bruts[,4])
DF <- affichage_concentration_Echantillons
###################################################
window_affichage_concentration_Echantillons <- tktoplevel()
#tkwm.title(window_affichage_concentration_Echantillons, "R\u00e9sultats des qPCR")
tkwm.title(window_affichage_concentration_Echantillons, texte33bis)
tkwm.geometry(window_affichage_concentration_Echantillons, "600x450")
frame <- ttkframe(window_affichage_concentration_Echantillons, padding = c(3,3,3,12))
tkpack(frame, expand = TRUE, fill = "both")
###################################################
frame_0 <- ttkframe(frame); tkpack(frame_0, fill = "x")
#label <- ttklabel(frame_0, text = "filtre:")
label <- ttklabel(frame_0, text = texte34)
tkpack(label, side = "left")
filter_var <- tclVar("")
filter_entry <- ttkentry(frame_0, textvariable = filter_var)
tkpack(filter_entry, side = "left")
###################################################
frame_1 <- ttkframe(frame)
tkpack(frame_1, expand = TRUE, fill = "both")
treeview <- ttktreeview(frame_1, columns = 1:ncol(DF),
#displaycolumns = 1:ncol(DF),
show = "headings", # not "tree"
selectmode = "browse") # single selection
addScrollbars(frame_1, treeview)
frame_2 <- ttkframe(frame); tkpack(frame_2, fill = "both")
Savefunctioncsv <- function(){
#### Select field to import ASCII profiles ####
#fil=if (interactive()) file.choose()
tt2 <- tktoplevel()
tkwm.geometry(tt2, "400x200")
#tkwm.title(tt2,"Exporter fichier.csv")
tkwm.title(tt2, texte35)
tkgrid(tklabel(tt2,text=""))
t1 <- tkframe(tt2)
#text1<-tklabel(t1,text="Quel est le s\u00e9parateur ?")
text1 <- tklabel(t1,text=texte36)
#sep1<-c("tab (tabulation)",", (virgule)","; (point virgule)",". (point)"," (espace)")
sep1 <- c(texte37,texte13,texte38,texte12,texte39)
sep2 <- tkwidget(t1,"ComboBox",editable=FALSE,values=sep1,height=3)
tkpack(text1,sep2,side="left")
tkgrid(t1)
t2 <- tkframe(tt2)
#text2<-tklabel(t2,text="Quel est le symbole d\u00e9cimal ?")
text2 <- tklabel(t2,text=texte11)
#dec1<-c(". (point)",", (virgule)")
dec1 <- c(texte12,texte13)
dec2 <- tkwidget(t2,"ComboBox",editable=FALSE,values=dec1,height=2)
tkpack(text2,dec2,side="left")
tkgrid(t2)
#t3<-tkframe(tt2)
#text3<-tklabel(t3,text="Do you have header")
#hea1 <- c("yes","no")
#hea2 <- tkwidget(t3,"ComboBox",editable=FALSE,values=hea1,height=2)
#tkpack(text3,hea2,side="left")
#tkgrid(t3)
tkgrid(tklabel(tt2,text=""))
#### Preview channels ####
view.channels <- function()
{
sep3 <-unlist(as.numeric(tcl(sep2,"getvalue"))+1 )
if(sep3==1) sep4 <- "\t"
if(sep3==2) sep4 <- ","
if(sep3==3) sep4 <- ";"
if(sep3==4) sep4 <- "."
if(sep3==5) sep4 <- " "
dec3 <-unlist(as.numeric(tcl(dec2,"getvalue"))+1 )
if(dec3==1) dec4 <- "."
if(dec3==2) dec4 <- ","
#hea3 <-unlist(as.numeric(tcl(hea2,"getvalue"))+1 )
#if(hea3==1) hea4<-TRUE
#if(hea3==2) hea4<-FALSE
dataExportees <- tclvalue(tkgetSaveFile())
dataexportees <- paste(dataExportees,".csv",sep="")
write.table(affichage_concentration_Echantillons,file = dataexportees,col.names=T,row.names=F,dec=dec4,sep=sep4)
tkdestroy(tt2)
}
#tkgrid(tkbutton(tt2,text="Exporter fichier",command=view.channels))
tkgrid(tkbutton(tt2,text=texte40,command=view.channels))
tkgrid(tklabel(tt2,text=""))
}
#Savecsv.but<-tkbutton(frame_2,text=" Exporter\ncsv ",command=Savefunctioncsv)
Savecsv.but <- tkbutton(frame_2,text=texte41,command=Savefunctioncsv)
tkgrid(Savecsv.but,row=1,column=2)
Savefunctionxlsx <- function(){
#Exportationfichierxlsx=tkmessageBox(title="Exporter fichier en xlsx", message=" Voulez-vous exporter votre fichier en xlsx ?",
# icon="info",type="yesno")
Exportationfichierxlsx <- tkmessageBox(title=texte42, message=texte43,
icon="info",type="yesno")
Exportationfichierxlsx1 <- tclvalue(Exportationfichierxlsx)
if(Exportationfichierxlsx1=="yes") {
dataExportees <- tclvalue(tkgetSaveFile())
dataexportees <- paste(dataExportees,".xlsx",sep="")
write.xlsx(affichage_concentration_Echantillons,file = dataexportees,col.names=T,row.names=F,sheetName="1")
}else{tkdestroy(Exportationfichierxlsx)}
}
#Savexlsx.but<-tkbutton(frame_2,text=" Exporter\nxlsx ",command=Savefunctionxlsx)
Savexlsx.but <- tkbutton(frame_2,text= texte44,command=Savefunctionxlsx)
tkgrid(Savexlsx.but,row=1,column=4)
###################################################
widths <- c(rep(100,dim(DF)[2])) #c(100,200) #rep(100,dim(DF)[2])) # hard coded
nms <- names(DF)
for(i in 1:dim(DF)[2]) {
tcl(treeview, "heading", i, text = nms[i])
tcl(treeview, "column", i, width = widths[i],
stretch = TRUE, anchor = "w")
}
###################################################
fillTable <- function(treeview, DF) {
children <- as.character(tcl(treeview, "children", ""))
for(i in children)
tcl(treeview, "delete", i)
#shade <- c("none", "gray")
for(i in seq_len(nrow(DF)))
tcl(treeview, "insert", "", "end",
text = "",
values = unlist(DF[i,]))
tktag.configure(treeview, "gray", background = "red")
}
###################################################
fillTable(treeview, DF)
## permet utiliser la commade filtre
cur_ind <- 1:nrow(DF)
tkbind(filter_entry, "<KeyRelease>", function(W, K) {
val <- tclvalue(tkget(W))
poss_vals <- apply(DF, 1, function(...)
paste(..., collapse = " "))
ind<- grep(val, poss_vals)
if(length(ind) == 0) ind <- 1:nrow(DF)
fillTable(treeview, DF[ind,])
})
} # fin de la function table
Calulechantillons_et_tableau_resultats <- function(){
calcul_echantillons()
Tableau_Echantillons_concentration()
}
Calcul_echantillons.but <- tkbutton(Interface_Total_qPCR,command=Calulechantillons_et_tableau_resultats)
tkconfigure(Calcul_echantillons.but,image=tkimage.create("photo",file=file.path(path.package("InterfaceqPCR"),"Tubes.gif",
fsep=.Platform$file.sep)))
tkgrid(Calcul_echantillons.but,row=15,column=3, columnspan=3)
##########################################################################################################
######
apropos <- function(){
aidefenetre <- tktoplevel()
#tkwm.title(aidefenetre," A propos de InterfaceqPCR")
tkwm.title(aidefenetre,texte6)
tkconfigure(aidefenetre,bg="gray80",cursor="hand2") # wheat1 hand2
# Taille
tkwm.geometry(aidefenetre, "500x600") # Largueur x hauteur
tkwm.resizable(aidefenetre,F,F)
# Police
font2 <- tkfont.create(family="times",size=14,weight="bold",slant="italic")
font3 <- tkfont.create(family="times",size=12,weight="bold")
path.logobatman <- file.path(path.package("InterfaceqPCR"),"a_laise_BZH2.gif", fsep=.Platform$file.sep)
mon.imagebatman <- tkimage.create("photo", file=path.logobatman )
montre.batman <- tklabel(aidefenetre, image=mon.imagebatman, background="white")
tkgrid(montre.batman,row=1, column=3,columnspan=2)
videaide <- tklabel(aidefenetre,text=" ",font=font2,bg="gray80")
tkgrid(videaide,row=2)
# message<-tklabel(aidefenetre,text="InterfaceqPCR\nTraitement des donn\u00e9es issues de la qPCR Version 1.0
# \nOlivier Le Goff
# \nLaboratoire EA CIDAM Clermont-Ferrand\nUniversit\u00e9 d'Auvergne\n2016",bg="gray80",font=font3)
#
message <- tklabel(aidefenetre,text=texte7,bg="gray80",font=font3)
tkgrid(message,row=3, column=3,columnspan=2)
path.logoimmunoaide <- file.path(path.package("InterfaceqPCR"),"logoEAUDA.gif", fsep=.Platform$file.sep)
mon.imageimmunoaide <- tkimage.create("photo", file=path.logoimmunoaide)
montre.imageimmunoaide <- tklabel(aidefenetre, image=mon.imageimmunoaide, background="white")
tkgrid(montre.imageimmunoaide,row=4, column=3)
fermeraide=function(){
tkdestroy(aidefenetre)
}
#Ok.butaide<-tkbutton(aidefenetre,text="Quitter",command=fermeraide,font=font2,foreground="Blue")
Ok.butaide <- tkbutton(aidefenetre,text=texte8, command=fermeraide,font=font2,foreground="Blue")
tkgrid(Ok.butaide,row=4, column=4)
}
fermeture_Interface_qPCR=function(){
tkdestroy(Interface_Total_qPCR)
Interface_qPCR_choix()
}
Fermeture_qPCR.but <- tkbutton(Interface_Total_qPCR,command=fermeture_Interface_qPCR)
tkconfigure(Fermeture_qPCR.but,image=tkimage.create("photo",file=file.path(path.package("InterfaceqPCR"),"start.gif",
fsep=.Platform$file.sep)))
tkgrid(Fermeture_qPCR.but,row=16,column=2)
Aide.but <- tkbutton(Interface_Total_qPCR,command=apropos)
tkconfigure(Aide.but,image=tkimage.create("photo",file=file.path(path.package("InterfaceqPCR"),"apropos.gif",
fsep=.Platform$file.sep)))
tkgrid(Aide.but,row=16,column=7)
} # fin de la fonction Interface_qPCR
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Defines functions Interface_qPCR
#
# # \\\||||||///
# # \\ ~ ~ //
# # ( @ @ )
# # ________________oOOo-(_)-oOOo________________
# # | |
# # | Interface qPCR package |
# # | Analyse des donnees qPCR |
# # | chargement fichier gamme etalon |
# # | chargement fichier echantillons |
# # | Decembre 2016 |
# # |______________________Oooo.__________________|
# # .oooO ( )
# # ( ) ) /
# # \ ( (_/
# # \_)
# #
# # Author: Olivier Le Goff
# ###############################################################################
# ###############################################################################
Interface_qPCR <- function(){
choix_langue<-texte1<-texte2<-texte3<-texte4<-texte5<-texte6<-texte7<-texte8<-texte9<-texte10<-texte11<-texte12<-texte13<-
texte14<-texte15<-texte16<-texte17<-texte18<-texte19<-texte20<-texte21<-texte22<-texte23<-texte24<-texte25<-
texte26<-texte27<-texte28<-texte29<-texte30<-texte31<-texte32<-texte33<-texte33bis<-texte34<-texte35<-texte36<-
texte37<-texte38<-texte39<-texte40<-texte41<-texte42<-texte43<-texte44<-texte45<-texte46<-texte47<-texte48<-
texte48bis<-texte49<-texte50<-texte51<-texte52<-texte52bis<-texte53<-texte54<-texte55<-texte56<-texte57<-
texte58<-texte59<-texte60<-texte61<-texte62<-Echantillons_bruts<-choixconcentration<-Condition<-regressionnontraite<-
dataimportees_echantillons<-data_moy_ADN_nontraite<-Efficacitenontraite<-regressionnontraite<-choixconcentration<-
Ct<-dataimportees_gamme_etalon<-couleur1_ech<-couleur1<-Nbechantillons2 <-NULL
#require(tcltk)
tclRequire("BWidget")
rm(list=ls())
if(exists("dataimportees_gamme_etalon")==TRUE) {rm(dataimportees_gamme_etalon, pos=1)}
if(exists("dataimportees_echantillons")==TRUE) {rm(dataimportees_echantillons, pos=1)}
couleur1 <<- "red"
couleur1_ech <<- "red"
Nbechantillons2 <<- NA
# D\u00e9but interface graphique
Interface_Total_qPCR <- tktoplevel()
#tkwm.title(Interface_Total_qPCR,"Interface qPCR \u00e9chantillons non trait\u00e9s au PMA")
tkwm.title(Interface_Total_qPCR,texte45)
tkconfigure(Interface_Total_qPCR,bg="wheat1",cursor="hand2")
# Taille
tkwm.geometry(Interface_Total_qPCR, "700x700") # Largueur x hauteur
tkwm.resizable(Interface_Total_qPCR,F,F)
# Police
fontHeading <- tkfont.create(family="times",size=20,weight="bold",slant="italic")
font2 <- tkfont.create(family="times",size=14,weight="bold",slant="italic")
font3 <- tkfont.create(family="times",size=12,weight="bold")
## Import xlsx file
importfilexlsx_gamme_etalon <- function(){
#require(xlsx)
Total_gamme_std <- matrix(c(".xlsx",".xlsx"),1, 2, byrow = TRUE)
fil <- if(interactive()) tk_choose.files(filters = Total_gamme_std)
# Detectionchargementxlsx <- loadedNamespaces()
# if(any(Detectionchargementxlsx =="xlsx") == TRUE){dataimportees_gamme_etalon=read.xlsx(fil[1],header=T, 1)
# } else {requireNamespace(readxl)
# dataimportees_gamme_etalon <- read_excel(fil[1])
# }
dataimportees_gamme_etalon=read.xlsx(fil[1],header=T, 1)
dataimportees_gamme_etalon <<- dataimportees_gamme_etalon
dataimportees_gamme_etalon <<- dataimportees_gamme_etalon
donnees1_gamme_etalon <- dataimportees_gamme_etalon
donnees1_gamme_etalon <<- donnees1_gamme_etalon
}
## Import xlsx file
importfilexlsx_echantillons <- function(){
#require(xlsx)
Total_echnoPMA <- matrix(c(".xlsx",".xlsx"),1, 2, byrow = TRUE)
fil_ech <- if(interactive()) tk_choose.files(filters = Total_echnoPMA)
#
# Detectionchargementxlsx <- loadedNamespaces()
# if(any(Detectionchargementxlsx =="xlsx") == TRUE){dataimportees_echantillons=read.xlsx(fil_ech[1],header=T, 1)
# } else {requireNamespace(readxl)
# dataimportees_echantillons <- read_excel(fil_ech[1])
# }
dataimportees_echantillons=read.xlsx(fil_ech[1],header=T, 1)
dataimportees_echantillons <<- dataimportees_echantillons
dataimportees_echantillons <<- dataimportees_echantillons
donnees1_echantillons <- dataimportees_echantillons
donnees1_echantillons <<- donnees1_echantillons
}
###########################################################################################
## Importer le fichier des donn\u00e9es brutes
#etape1=tklabel(Interface_Total_qPCR, text="1 Importer les fichiers",font=fontHeading,foreground="chocolate4",bg="wheat1")
etape1 <- tklabel(Interface_Total_qPCR, text=texte18,font=fontHeading,foreground="chocolate4",bg="wheat1")
tkgrid(etape1, row=1, columnspan=4, sticky ="w")
## Fichier contenant la gamme \u00e9talon
#etape11=tklabel(Interface_Total_qPCR, text="Fichier Gamme \u00e9talon",font=font2,foreground="chocolate4",bg="wheat1")
etape11 <- tklabel(Interface_Total_qPCR, text=texte19,font=font2,foreground="chocolate4",bg="wheat1")
tkgrid(etape11, row=2, columnspan=4)
#import xlsx file
IMPORTxlsx.but <- tkbutton(Interface_Total_qPCR,command=importfilexlsx_gamme_etalon)
tkconfigure(IMPORTxlsx.but,image=tkimage.create("photo",file=file.path(path.package("InterfaceqPCR"),"xlsx.gif",
fsep=.Platform$file.sep)))
tkgrid(IMPORTxlsx.but,row=3,column=4)
# V\u00e9rification de l importation du fichier de donn\u00e9es brutes
Verif_import23 <- function(){
#if(exists("dataimportees_gamme_etalon")==TRUE) {"Oui"} else {"Non"}
if(exists("dataimportees_gamme_etalon")==TRUE) {texte15}else {texte16}
}
Verif_couleur <- function()
{
couleur1 <- if(exists("dataimportees_gamme_etalon")==TRUE) {"green"}else {"red"}
couleur1 <<- couleur1
}
Verif_couleur()
Verifimport2 <- Verif_import23()
#ImportationFichiertest<-tklabel(Interface_Total_qPCR, text=" Fichier cr\u00e9\u00e9 :" ,bg="wheat1")
ImportationFichiertest <- tklabel(Interface_Total_qPCR, text=texte23 ,bg="wheat1")
tkgrid(ImportationFichiertest, row=3, column=5, sticky="e")
ImportationFichiercase <- tkentry(Interface_Total_qPCR,width=10,foreground=couleur1, bg="black", textvariable=tclVar(Verifimport2))
tkgrid(ImportationFichiercase,row=3,column=6)
# Actualiser la v\u00e9rif du fichier importe
Actualisationimport <- function(){
Verif_import23 <- function(){
#if(exists("dataimportees_gamme_etalon")==TRUE) {"Oui"} else {"Non"}
if(exists("dataimportees_gamme_etalon")==TRUE) {texte15}else {texte16}
}
Verif_couleur <- function()
{
couleur1 <- if(exists("dataimportees_gamme_etalon")==TRUE) {"green"}else {"red"}
couleur1 <<- couleur1
}
Verif_couleur()
Verifimport22 <- Verif_import23()
#ImportationFichiertest<-tklabel(Interface_Total_qPCR, text=" Fichier cr\u00e9\u00e9 :" ,bg="wheat1")
ImportationFichiertest <- tklabel(Interface_Total_qPCR, text=texte23,bg="wheat1")
tkgrid(ImportationFichiertest, row=3, column=5, sticky="e")
ImportationFichiercase <- tkentry(Interface_Total_qPCR,width=10,bg="black",foreground=couleur1, textvariable=tclVar(Verifimport22))
tkgrid(ImportationFichiercase,row=3,column=6)
}
#Actualiser.but<-tkbutton(Interface_Total_qPCR,text="Actualiser", command=Actualisationimport)
Actualiser.but <- tkbutton(Interface_Total_qPCR,text=texte24, command=Actualisationimport)
tkgrid(Actualiser.but,row=3,column=7)
## Fichier contenant les echantillons
vide1 <- tklabel(Interface_Total_qPCR, text=" ",font=font2,foreground="chocolate4",bg="wheat1")
tkgrid(vide1, row=4, columnspan=4)
#etape1111=tklabel(Interface_Total_qPCR, text="Fichier Echantillons",font=font2,foreground="chocolate4",bg="wheat1")
etape1111 <- tklabel(Interface_Total_qPCR, text=texte25,font=font2,foreground="chocolate4",bg="wheat1")
tkgrid(etape1111, row=5, columnspan=4)
#import xlsx file echantillons
IMPORTxlsx_echantillons.but <- tkbutton(Interface_Total_qPCR,command=importfilexlsx_echantillons)
tkconfigure(IMPORTxlsx_echantillons.but,image=tkimage.create("photo",file=file.path(path.package("InterfaceqPCR"),"xlsx.gif",
fsep=.Platform$file.sep)))
tkgrid(IMPORTxlsx_echantillons.but,row=6,column=4)
# V\u00e9rification de l'importation du fichier de donn\u00e9es brutes
Verif_import24 <- function(){
#if(exists("dataimportees_gamme_etalon")==TRUE) {"Oui"} else {"Non"}
if(exists("dataimportees_echantillons")==TRUE) {texte15}else {texte16}
}
Verif_couleur_ech <- function()
{
couleur1_ech <- if(exists("dataimportees_echantillons")==TRUE) {"green"}else {"red"}
couleur1_ech <<- couleur1_ech
}
Verif_couleur_ech()
Verifimport_ech2 <- Verif_import24()
#ImportationFichierechantillons<-tklabel(Interface_Total_qPCR, text=" Fichier cr\u00e9\u00e9 :" ,bg="wheat1")
ImportationFichierechantillons <- tklabel(Interface_Total_qPCR, text=texte23 ,bg="wheat1")
tkgrid(ImportationFichierechantillons, row=6, column=5, sticky="e")
ImportationFichier_ech_case <- tkentry(Interface_Total_qPCR,width=10,foreground=couleur1_ech, bg="black", textvariable=tclVar(Verifimport_ech2))
tkgrid(ImportationFichier_ech_case,row=6,column=6)
# Actualiser la v\u00e9rif du fichier importe
Actualisationimport_ech <- function(){
#if(exists("dataimportees_echantillons")==TRUE) {"Oui"} else {"Non"}
if(exists("dataimportees_echantillons")==TRUE) {texte15}else {texte16}
Verif_import24 <- function(){
#if(exists("dataimportees_gamme_etalon")==TRUE) {"Oui"} else {"Non"}
if(exists("dataimportees_echantillons")==TRUE) {texte15}else {texte16}
}
Verif_couleur_ech <- function()
{
couleur1_ech <- if(exists("dataimportees_echantillons")==TRUE) {"green"}else {"red"}
couleur1_ech <<- couleur1_ech
}
Verif_couleur_ech()
Verifimport_ech22 <- Verif_import24()
#ImportationFichierechantillons<-tklabel(Interface_Total_qPCR, text=" Fichier cr\u00e9\u00e9 :" ,bg="wheat1")
ImportationFichierechantillons <- tklabel(Interface_Total_qPCR, text=texte23 ,bg="wheat1")
tkgrid(ImportationFichierechantillons, row=6, column=5, sticky="e")
ImportationFichier_ech_case <- tkentry(Interface_Total_qPCR,width=10, foreground=couleur1_ech, bg="black", textvariable=tclVar(Verifimport_ech22))
tkgrid(ImportationFichier_ech_case,row=6,column=6)
###
Calcul_Nb_echantillons2 = function(){
if(exists("dataimportees_echantillons")==FALSE) {" "}else{
Nbechantillons <- subset(dataimportees_echantillons, ! Condition %in% c("PMA"))
Nbechantillons2 <- length(Nbechantillons$Nom_Echantillon)
Nbechantillons2 <<- Nbechantillons2
}
}
Calcul_Nb_echantillons = function(){
if(exists("dataimportees_echantillons")==FALSE) {" "} else {Calcul_Nb_echantillons2()}
}
ImportationNbFichier_ech_case <- tkentry(Interface_Total_qPCR,width=10,foreground=couleur1_ech,
font=font3, bg="black",
textvariable=tclVar(Calcul_Nb_echantillons()))
tkgrid(ImportationNbFichier_ech_case,row=14,column=3)
}
#Actualiserech.but<-tkbutton(Interface_Total_qPCR,text="Actualiser", command=Actualisationimport_ech)
Actualiserech.but <- tkbutton(Interface_Total_qPCR,text=texte24, command=Actualisationimport_ech)
tkgrid(Actualiserech.but,row=6,column=7)
##################################################################################################
## Importer le fichier des donn\u00e9es brutes
vide2 <- tklabel(Interface_Total_qPCR, text="",font=fontHeading,foreground="chocolate4",bg="wheat1")
tkgrid(vide2, row=7, columnspan=4)
#etape2=tklabel(Interface_Total_qPCR, text="2 Droite de r\u00e9gression",font=fontHeading,foreground="chocolate4",bg="wheat1")
etape2 <- tklabel(Interface_Total_qPCR, text=texte27,font=fontHeading,foreground="chocolate4",bg="wheat1")
tkgrid(etape2, row=8, columnspan=4, sticky="w")
## Ajout du choix de la concentration
#etape21=tklabel(Interface_Total_qPCR, text="Concentration en :",font=font2,foreground="chocolate4",bg="wheat1")
etape21 <- tklabel(Interface_Total_qPCR, text=texte51,font=font2,foreground="chocolate4",bg="wheat1")
tkgrid(etape21, row=9, column=2)
# radio boutons
rb1_UFC <- tkradiobutton(Interface_Total_qPCR, font=font3,foreground="black",bg="wheat1")
rb2_copies <- tkradiobutton(Interface_Total_qPCR, font=font3,foreground="black",bg="wheat1")
# Choix par d\u00e9faut
rbValue <- tclVar(texte52)
# config des boutons radio. Une seule variable tcl pour 2 boutons
#tkconfigure(rb2_copies,variable=rbValue,value=" UFC/mL", text=" UFC/mL")
tkconfigure(rb1_UFC,variable=rbValue,value=texte52, text=texte52)
#tkconfigure(rb2_copies,variable=rbValue,value="Nb copies/mL", text="Nb copies/mL")
tkconfigure(rb2_copies,variable=rbValue,value=texte53, text=texte53)
tkgrid(rb1_UFC,row=9, column=3)
tkgrid(rb2_copies,row=9,column=5)
#etape212=tklabel(Interface_Total_qPCR, text="ou",font=font3,foreground="chocolate4",bg="wheat1")
etape212=tklabel(Interface_Total_qPCR, text=texte22,font=font3,foreground="chocolate4",bg="wheat1")
tkgrid(etape212,row=9,column=4)
OnOK <- function() {
#message<-paste("Votre choix est :", tclvalue(rbValue))
message<-paste(texte54, tclvalue(rbValue))
tkmessageBox(title="Validation", message=message, icon="info", type="ok")
choixconcentration <<-tclvalue(rbValue)
}
OK.but <- tkbutton(Interface_Total_qPCR, text="OK", command=OnOK)
tkgrid(OK.but,row=9,column=6)
# Calcul et tracage de droite de regression issue des standards
Calcul_regression <- function(){
#library(reshape2)
#library(plyr)
fusion_data <- dataimportees_gamme_etalon
head(fusion_data)
# Calculer moyenne et ecart type par Standard
data_moy_sd <- ddply(fusion_data,c("Numero","Standard","log10_Sdt","Condition"),summarise,
Moy=mean(Ct,na.rm=TRUE),
sd=sd(Ct,na.rm=TRUE))
data_moy_sd
data_moy_sd <<- data_moy_sd[complete.cases(data_moy_sd), ]
# equation de la droite de regression ADN non traite issue de data_moy_sd
data_moy_ADN_nontraite <- subset(data_moy_sd, Condition=="Total")
data_moy_ADN_nontraite <<- data_moy_ADN_nontraite
regressionnontraite <- lm(data_moy_ADN_nontraite$Moy~data_moy_ADN_nontraite$log10_Sdt,data_moy_ADN_nontraite)
regressionnontraite <<- regressionnontraite
pentenontraite <- format(regressionnontraite$coefficients[2], digits = 3)
interceptionnontraite <- format(regressionnontraite$coefficients[1], digits = 4)
r2nontraite <- format(summary(regressionnontraite)$r.squared, digits = 3)
r2nontraite <<- r2nontraite
Efficacitenontraite <- format((-1+(10^(-1/summary(regressionnontraite)$coefficients[2])))*100, digits = 3)
if(Efficacitenontraite>100){Efficacitenontraite=100}else{Efficacitenontraite}
Efficacitenontraite <<- Efficacitenontraite
equation_droitenontraite <- paste("y =",interceptionnontraite , pentenontraite ,"x" )
R2equation_droitenontraite <- paste("R2 =", r2nontraite)
Efficaciteequation_droitenontraite <- paste("E =", Efficacitenontraite,"%")
equation_droitenontraite <<- equation_droitenontraite
R2equation_droitenontraite <<- R2equation_droitenontraite
Efficaciteequation_droitenontraite <<- Efficaciteequation_droitenontraite
}
graphique_regression <- function(){
#library(tkrplot)
fenetre_graphique <- tktoplevel()
#tkwm.title(fenetre_graphique,"Droite de regression issue des Standards qPCR")
tkwm.title(fenetre_graphique, texte28)
tkconfigure(fenetre_graphique,bg="wheat1",cursor="hand2")
# Taille
tkwm.geometry(fenetre_graphique, "625x700") # Largueur x hauteur
tkwm.resizable(fenetre_graphique,F,F)
image1plot <- function(){
#
# Condition si concentration en UFC/mL
if(choixconcentration == texte52) {
###########
XX <- log10(data_moy_ADN_nontraite$Standard)
#XX<-data_moy_ADN_nontraite$Standard
YY <- data_moy_ADN_nontraite$Moy
REGRESSION_PENTE <- format(regressionnontraite$coefficients[2], digits = 3)
REGRESSION_INTERCEPTION <- format(regressionnontraite$coefficients[1], digits = 3)
r2STD <- format(summary(regressionnontraite)$r.squared, digits = 3)
Efficacitetrace <- Efficacitenontraite
LODtracetraite <- ceiling(10^(3*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
LOQtracetraite <- ceiling(10^(10*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
par(lab=c(10,10,10),oma=c(5,2,0,0))
plot(XX,YY,cex.axis=0.7,las=1,xlim=c(0,10),ylim=c(0,50),
pch=16,col="red",
main="",
xlab=" ",
ylab=expression(paste(C[t], "value")))
#abline(lm(data_moy_ADN_nontraite$Moy~data_moy_ADN_nontraite$log10_Sdt,data_moy_ADN_nontraite))
#ecarts-types mis sur le barplot
arrows(XX, data_moy_ADN_nontraite$Moy + data_moy_ADN_nontraite$sd,
XX, data_moy_ADN_nontraite$Moy - data_moy_ADN_nontraite$sd,
length = 0.05, # width of the arrowhead
angle = 90,
code = 3)
abline(b = REGRESSION_PENTE, a = REGRESSION_INTERCEPTION,col="black")
legend("topright",legend=paste("y =", REGRESSION_PENTE ,"x + ",REGRESSION_INTERCEPTION, "\nR2 =", r2STD,
"\nE=",Efficacitetrace, " %",
"\nLOD=",LODtracetraite, texte52,
"\nLOQ=",LOQtracetraite, texte52),bty="n",cex=0.75)
axis(1,at=c(0,sort(XX)),labels=format(c(0,sort(data_moy_ADN_nontraite$Standard)),scientific=TRUE,digits = 3),
line=3,col="blue",col.ticks="blue",col.axis="blue",cex.axis=0.75, las=2)
# text(-1,-10,"UFC/mL", cex= 0.8,col="blue",xpd=TRUE)
text(-1,-10, texte52 , cex= 0.8,col="blue",xpd=TRUE)
#text(-1,-6,expression(paste(Log[10],"(UFC/mL)")), cex= 0.7,col="black",xpd=TRUE)
text(-1,-6, texte52bis , cex= 0.7,col="black",xpd=TRUE)
#
#
# si condition concentration est Nb copies/mL
}else{
###########
XX <- log10(data_moy_ADN_nontraite$Standard)
#XX<-data_moy_ADN_nontraite$Standard
YY <- data_moy_ADN_nontraite$Moy
REGRESSION_PENTE <- format(regressionnontraite$coefficients[2], digits = 3)
REGRESSION_INTERCEPTION <- format(regressionnontraite$coefficients[1], digits = 3)
r2STD <- format(summary(regressionnontraite)$r.squared, digits = 3)
Efficacitetrace <- Efficacitenontraite
LODtracetraite <- ceiling(10^(3*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
LOQtracetraite <- ceiling(10^(10*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
par(lab=c(10,10,10),oma=c(5,2,0,0))
plot(XX,YY,cex.axis=0.7,las=1,xlim=c(0,10),ylim=c(0,50),
pch=16,col="red",
main="",
xlab=" ",
ylab=expression(paste(C[t], "value")))
#abline(lm(data_moy_ADN_nontraite$Moy~data_moy_ADN_nontraite$log10_Sdt,data_moy_ADN_nontraite))
#ecarts-types mis sur le barplot
arrows(XX, data_moy_ADN_nontraite$Moy + data_moy_ADN_nontraite$sd,
XX, data_moy_ADN_nontraite$Moy - data_moy_ADN_nontraite$sd,
length = 0.05, # width of the arrowhead
angle = 90,
code = 3)
abline(b = REGRESSION_PENTE, a = REGRESSION_INTERCEPTION,col="black")
legend("topright",legend=paste("y =", REGRESSION_PENTE ,"x + ",REGRESSION_INTERCEPTION, "\nR2 =", r2STD,
"\nE=",Efficacitetrace, " %",
"\nLOD=",LODtracetraite, "copies/mL",
"\nLOQ=",LOQtracetraite, "copies/mL"),bty="n",cex=0.75)
axis(1,at=c(0,sort(XX)),labels=format(c(0,sort(data_moy_ADN_nontraite$Standard)),scientific=TRUE,digits=3),
line=3,col="blue",col.ticks="blue",col.axis="blue",cex.axis=0.75, las=2)
text(-1,-10,"copies/mL", cex= 0.8,col="blue",xpd=TRUE)
text(-1,-6,expression(paste(Log[10], " (copies/mL)")), cex= 0.7,col="black",xpd=TRUE)
}
} # fin fonction image1
image1 <- tkrplot(fenetre_graphique,fun=image1plot,hscale=1.9,vscale=1.9)
tkgrid(image1,columnspan=5,rowspan=4)
exportertiffplot <- function() {
# Exportationfichiertiff1=tkmessageBox(title="Enregistrer en .tiff", message="Voulez-vous enregistrer en .tiff ?",
# icon="info",type="yesno")
Exportationfichiertiff1=tkmessageBox(title=texte55, message=texte56 ,
icon="info",type="yesno")
Exportationfichiertiff11<-tclvalue(Exportationfichiertiff1)
if(Exportationfichiertiff11=="yes" & choixconcentration ==texte52) {
XX <- log10(data_moy_ADN_nontraite$Standard)
#XX<-data_moy_ADN_nontraite$Standard
YY <- data_moy_ADN_nontraite$Moy
REGRESSION_PENTE <- format(regressionnontraite$coefficients[2], digits = 3)
REGRESSION_INTERCEPTION <- format(regressionnontraite$coefficients[1], digits = 3)
r2STD <- format(summary(regressionnontraite)$r.squared, digits = 3)
Efficacitetrace <- Efficacitenontraite
LODtracetraite <- ceiling(10^(3*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
LOQtracetraite <- ceiling(10^(10*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
FigureExportee_Tiff <- tclvalue(tkgetSaveFile())
figureExportee_Tiff <- paste(FigureExportee_Tiff,".tiff",sep="")
Standard_curves_UFC_mL <- function() {
par(lab=c(10,10,10),oma=c(5,2,0,0))
plot(XX,YY,cex.axis=0.7,las=1,xlim=c(0,10),ylim=c(0,50),
pch=16,col="red",
main="",
xlab=" ",
ylab=expression(paste(C[t], "value")))
#abline(lm(data_moy_ADN_nontraite$Moy~data_moy_ADN_nontraite$log10_Sdt,data_moy_ADN_nontraite))
arrows(XX, data_moy_ADN_nontraite$Moy + data_moy_ADN_nontraite$sd,
XX, data_moy_ADN_nontraite$Moy - data_moy_ADN_nontraite$sd,
length = 0.05, # width of the arrowhead
angle = 90,
code = 3)
abline(b = REGRESSION_PENTE, a = REGRESSION_INTERCEPTION,col="black")
legend("topright",legend=paste("y =", REGRESSION_PENTE ,"x + ",REGRESSION_INTERCEPTION, "\nR2 =", r2STD,
"\nE=",Efficacitetrace, " %",
"\nLOD=",LODtracetraite, texte52,
"\nLOQ=",LOQtracetraite, texte52),bty="n",cex=0.75)
axis(1,at=c(0,sort(XX)),labels=format(c(0,sort(data_moy_ADN_nontraite$Standard)),scientific=TRUE,digits = 3),
line=3,col="blue",col.ticks="blue",col.axis="blue",cex.axis=0.75, las=2)
# text(-1,-10,"UFC/mL", cex= 0.8,col="blue",xpd=TRUE)
text(-1,-10, texte52 , cex= 0.8,col="blue",xpd=TRUE)
#text(-1,-6,expression(paste(Log[10],"(UFC/mL)")), cex= 0.7,col="black",xpd=TRUE)
text(-1,-6, texte52bis, cex= 0.7,col="black",xpd=TRUE)
}
tiff(filename=figureExportee_Tiff, compression = "lzw",
height=18, width=18, units="cm", res=400)
Standard_curves_UFC_mL()
dev.off()
}else{
if(Exportationfichiertiff11=="yes" & choixconcentration == texte53){
XX <- log10(data_moy_ADN_nontraite$Standard)
#XX<-data_moy_ADN_nontraite$Standard
YY <- data_moy_ADN_nontraite$Moy
REGRESSION_PENTE <- format(regressionnontraite$coefficients[2], digits = 3)
REGRESSION_INTERCEPTION <- format(regressionnontraite$coefficients[1], digits = 3)
r2STD <- format(summary(regressionnontraite)$r.squared, digits = 3)
Efficacitetrace <- Efficacitenontraite
LODtracetraite <- ceiling(10^(3*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
LOQtracetraite <- ceiling(10^(10*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
FigureExportee_Tiff <- tclvalue(tkgetSaveFile())
figureExportee_Tiff <- paste(FigureExportee_Tiff,".tiff",sep="")
Standard_curves_copies_mL <- function() {
par(lab=c(10,10,10),oma=c(5,2,0,0))
plot(XX,YY,cex.axis=0.7,las=1,xlim=c(0,10),ylim=c(0,50),
pch=16,col="red",
main="",
xlab="",
ylab=expression(paste(C[t], "value")))
#abline(lm(data_moy_ADN_nontraite$Moy~data_moy_ADN_nontraite$log10_Sdt,data_moy_ADN_nontraite))
arrows(XX, data_moy_ADN_nontraite$Moy + data_moy_ADN_nontraite$sd,
XX, data_moy_ADN_nontraite$Moy - data_moy_ADN_nontraite$sd,
length = 0.05, # width of the arrowhead
angle = 90,
code = 3)
abline(b = REGRESSION_PENTE, a = REGRESSION_INTERCEPTION,col="black")
legend("topright",legend=paste("y =", REGRESSION_PENTE ,"x + ",REGRESSION_INTERCEPTION, "\nR2 =", r2STD,
"\nE=",Efficacitetrace, " %",
"\nLOD=",LODtracetraite, "copies/mL",
"\nLOQ=",LOQtracetraite, "copies/mL"),bty="n",cex=0.75)
axis(1,at=c(0,sort(XX)),labels=format(c(0,sort(data_moy_ADN_nontraite$Standard)),scientific=TRUE,digits=3),
line=3,col="blue",col.ticks="blue",col.axis="blue",cex.axis=0.75, las=2)
text(-1,-10,"copies/mL", cex= 0.8,col="blue",xpd=TRUE)
text(-1,-6,expression(paste(Log[10], " (copies/mL)")), cex= 0.7,col="black",xpd=TRUE)
}
tiff(filename=figureExportee_Tiff, compression = "lzw",
height=18, width=18, units="cm", res=400)
Standard_curves_copies_mL()
dev.off()
}else{}
}
}
Export_Tiff.but <- tkbutton(fenetre_graphique, command=exportertiffplot)
tkconfigure(Export_Tiff.but,image=tkimage.create("photo",file=file.path(path.package("InterfaceqPCR"),"tiff.gif",
fsep=.Platform$file.sep)))
tkgrid(Export_Tiff.but, row=4, column=0)
exporterjpegplot <- function() {
Exportationfichierjpeg1=tkmessageBox(title= texte57, message= texte58,
icon="info",type="yesno")
Exportationfichierjpeg11<-tclvalue(Exportationfichierjpeg1)
if(Exportationfichierjpeg11=="yes" & choixconcentration == texte52) {
XX <- log10(data_moy_ADN_nontraite$Standard)
#XX<-data_moy_ADN_nontraite$Standard
YY <- data_moy_ADN_nontraite$Moy
REGRESSION_PENTE <- format(regressionnontraite$coefficients[2], digits = 3)
REGRESSION_INTERCEPTION <- format(regressionnontraite$coefficients[1], digits = 3)
r2STD <- format(summary(regressionnontraite)$r.squared, digits = 3)
Efficacitetrace <- Efficacitenontraite
LODtracetraite <- ceiling(10^(3*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
LOQtracetraite <- ceiling(10^(10*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
FigureExportee_Jpeg <- tclvalue(tkgetSaveFile())
figureExportee_Jpeg <- paste(FigureExportee_Jpeg,".jpeg",sep="")
Standard_curves_UFC_mL <- function() {
par(lab=c(10,10,10),oma=c(5,2,0,0))
plot(XX,YY,cex.axis=0.7,las=1,xlim=c(0,10),ylim=c(0,50),
pch=16,col="red",
main="",
xlab=" ",
ylab=expression(paste(C[t], "value")))
#abline(lm(data_moy_ADN_nontraite$Moy~data_moy_ADN_nontraite$log10_Sdt,data_moy_ADN_nontraite))
arrows(XX, data_moy_ADN_nontraite$Moy + data_moy_ADN_nontraite$sd,
XX, data_moy_ADN_nontraite$Moy - data_moy_ADN_nontraite$sd,
length = 0.05, # width of the arrowhead
angle = 90,
code = 3)
abline(b = REGRESSION_PENTE, a = REGRESSION_INTERCEPTION,col="black")
legend("topright",legend=paste("y =", REGRESSION_PENTE ,"x + ",REGRESSION_INTERCEPTION, "\nR2 =", r2STD,
"\nE=",Efficacitetrace, " %",
"\nLOD=",LODtracetraite, texte52,
"\nLOQ=",LOQtracetraite, texte52),bty="n",cex=0.75)
axis(1,at=c(0,sort(XX)),labels=format(c(0,sort(data_moy_ADN_nontraite$Standard)),scientific=TRUE,digits = 3),
line=3,col="blue",col.ticks="blue",col.axis="blue",cex.axis=0.75, las=2)
# text(-1,-10,"UFC/mL", cex= 0.8,col="blue",xpd=TRUE)
text(-1,-10, texte52, cex= 0.8,col="blue",xpd=TRUE)
#text(-1,-6,expression(paste(Log[10],"(UFC/mL)")), cex= 0.7,col="black",xpd=TRUE)
text(-1,-6, texte52bis , cex= 0.7,col="black",xpd=TRUE)
}
jpeg(filename=figureExportee_Jpeg, height=18, width=18, units="cm", res=400)
Standard_curves_UFC_mL()
dev.off()
}else{
if(Exportationfichierjpeg11=="yes" & choixconcentration == texte53){
XX <- log10(data_moy_ADN_nontraite$Standard)
#XX<-data_moy_ADN_nontraite$Standard
YY <- data_moy_ADN_nontraite$Moy
REGRESSION_PENTE <- format(regressionnontraite$coefficients[2], digits = 3)
REGRESSION_INTERCEPTION <- format(regressionnontraite$coefficients[1], digits = 3)
r2STD <- format(summary(regressionnontraite)$r.squared, digits = 3)
Efficacitetrace <- Efficacitenontraite
LODtracetraite <- ceiling(10^(3*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
LOQtracetraite <- ceiling(10^(10*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
FigureExportee_Jpeg <- tclvalue(tkgetSaveFile())
figureExportee_Jpeg <- paste(FigureExportee_Jpeg,".jpeg",sep="")
Standard_curves_copies_mL <- function() {
par(lab=c(10,10,10),oma=c(5,2,0,0))
plot(XX,YY,cex.axis=0.7,las=1,xlim=c(0,10),ylim=c(0,50),
pch=16,col="red",
main="",
xlab="",
ylab=expression(paste(C[t], "value")))
#abline(lm(data_moy_ADN_nontraite$Moy~data_moy_ADN_nontraite$log10_Sdt,data_moy_ADN_nontraite))
arrows(XX, data_moy_ADN_nontraite$Moy + data_moy_ADN_nontraite$sd,
XX, data_moy_ADN_nontraite$Moy - data_moy_ADN_nontraite$sd,
length = 0.05, # width of the arrowhead
angle = 90,
code = 3)
abline(b = REGRESSION_PENTE, a = REGRESSION_INTERCEPTION,col="black")
legend("topright",legend=paste("y =", REGRESSION_PENTE ,"x + ",REGRESSION_INTERCEPTION, "\nR2 =", r2STD,
"\nE=",Efficacitetrace, " %",
"\nLOD=",LODtracetraite, "copies/mL",
"\nLOQ=",LOQtracetraite, "copies/mL"),bty="n",cex=0.75)
axis(1,at=c(0,sort(XX)),labels=format(c(0,sort(data_moy_ADN_nontraite$Standard)),scientific=TRUE,digits=3),
line=3,col="blue",col.ticks="blue",col.axis="blue",cex.axis=0.75, las=2)
text(-1,-10,"copies/mL", cex= 0.8,col="blue",xpd=TRUE)
text(-1,-6,expression(paste(Log[10], " (copies/mL)")), cex= 0.7,col="black",xpd=TRUE)
}
jpeg(filename=figureExportee_Jpeg, height=18, width=18, units="cm", res=400)
Standard_curves_copies_mL()
dev.off()
}else{}
}
}
Export_jpeg.but <- tkbutton(fenetre_graphique, command=exporterjpegplot)
tkconfigure(Export_jpeg.but,image=tkimage.create("photo",file=file.path(path.package("InterfaceqPCR"),"jpg.gif",
fsep=.Platform$file.sep)))
tkgrid(Export_jpeg.but, row=4, column=1)
exporterpdfplot <- function() {
Exportationfichierpdf1=tkmessageBox(title= texte59, message= texte60,
icon="info",type="yesno")
Exportationfichierpdf11<-tclvalue(Exportationfichierpdf1)
if(Exportationfichierpdf11=="yes" & choixconcentration == texte52) {
XX <- log10(data_moy_ADN_nontraite$Standard)
#XX<-data_moy_ADN_nontraite$Standard
YY <- data_moy_ADN_nontraite$Moy
REGRESSION_PENTE <- format(regressionnontraite$coefficients[2], digits = 3)
REGRESSION_INTERCEPTION <- format(regressionnontraite$coefficients[1], digits = 3)
r2STD <- format(summary(regressionnontraite)$r.squared, digits = 3)
Efficacitetrace <- Efficacitenontraite
LODtracetraite <- ceiling(10^(3*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
LOQtracetraite <- ceiling(10^(10*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
FigureExportee_Pdf <- tclvalue(tkgetSaveFile())
figureExportee_Pdf <- paste(FigureExportee_Pdf,".pdf",sep="")
Standard_curves_UFC_mL <- function() {
par(lab=c(10,10,10),oma=c(5,2,0,0))
plot(XX,YY,cex.axis=0.7,las=1,xlim=c(0,10),ylim=c(0,50),
pch=16,col="red",
main="",
xlab=" ",
ylab=expression(paste(C[t], "value")))
#abline(lm(data_moy_ADN_nontraite$Moy~data_moy_ADN_nontraite$log10_Sdt,data_moy_ADN_nontraite))
arrows(XX, data_moy_ADN_nontraite$Moy + data_moy_ADN_nontraite$sd,
XX, data_moy_ADN_nontraite$Moy - data_moy_ADN_nontraite$sd,
length = 0.05, # width of the arrowhead
angle = 90,
code = 3)
abline(b = REGRESSION_PENTE, a = REGRESSION_INTERCEPTION,col="black")
legend("topright",legend=paste("y =", REGRESSION_PENTE ,"x + ",REGRESSION_INTERCEPTION, "\nR2 =", r2STD,
"\nE=",Efficacitetrace, " %",
"\nLOD=",LODtracetraite, texte52,
"\nLOQ=",LOQtracetraite, texte52),bty="n",cex=0.75)
axis(1,at=c(0,sort(XX)),labels=format(c(0,sort(data_moy_ADN_nontraite$Standard)),scientific=TRUE,digits = 3),
line=3,col="blue",col.ticks="blue",col.axis="blue",cex.axis=0.75, las=2)
# text(-1,-10,"UFC/mL", cex= 0.8,col="blue",xpd=TRUE)
text(-1,-10, texte52 , cex= 0.8,col="blue",xpd=TRUE)
#text(-1,-6,expression(paste(Log[10],"(UFC/mL)")), cex= 0.7,col="black",xpd=TRUE)
text(-1,-6, texte52bis , cex= 0.7,col="black",xpd=TRUE)
}
pdf(file=figureExportee_Pdf, paper="a4r", height=9, width=9)
Standard_curves_UFC_mL()
dev.off()
}else{
if(Exportationfichierpdf11=="yes" & choixconcentration ==texte53){
XX <- log10(data_moy_ADN_nontraite$Standard)
#XX<-data_moy_ADN_nontraite$Standard
YY <- data_moy_ADN_nontraite$Moy
REGRESSION_PENTE <- format(regressionnontraite$coefficients[2], digits = 3)
REGRESSION_INTERCEPTION <- format(regressionnontraite$coefficients[1], digits = 3)
r2STD <- format(summary(regressionnontraite)$r.squared, digits = 3)
Efficacitetrace <- Efficacitenontraite
LODtracetraite <- ceiling(10^(3*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
LOQtracetraite <- ceiling(10^(10*(summary.lm(regressionnontraite)$coefficients[1,2])/abs(regressionnontraite$coefficients[2])))
FigureExportee_Pdf <- tclvalue(tkgetSaveFile())
figureExportee_Pdf <- paste(FigureExportee_Pdf,".pdf",sep="")
Standard_curves_copies_mL <- function() {
par(lab=c(10,10,10),oma=c(5,2,0,0))
plot(XX,YY,cex.axis=0.7,las=1,xlim=c(0,10),ylim=c(0,50),
pch=16,col="red",
main="",
xlab="",
ylab=expression(paste(C[t], "value")))
#abline(lm(data_moy_ADN_nontraite$Moy~data_moy_ADN_nontraite$log10_Sdt,data_moy_ADN_nontraite))
arrows(XX, data_moy_ADN_nontraite$Moy + data_moy_ADN_nontraite$sd,
XX, data_moy_ADN_nontraite$Moy - data_moy_ADN_nontraite$sd,
length = 0.05, # width of the arrowhead
angle = 90,
code = 3)
abline(b = REGRESSION_PENTE, a = REGRESSION_INTERCEPTION,col="black")
legend("topright",legend=paste("y =", REGRESSION_PENTE ,"x + ",REGRESSION_INTERCEPTION, "\nR2 =", r2STD,
"\nE=",Efficacitetrace, " %",
"\nLOD=",LODtracetraite, "copies/mL",
"\nLOQ=",LOQtracetraite, "copies/mL"),bty="n",cex=0.75)
axis(1,at=c(0,sort(XX)),labels=format(c(0,sort(data_moy_ADN_nontraite$Standard)),scientific=TRUE,digits=3),
line=3,col="blue",col.ticks="blue",col.axis="blue",cex.axis=0.75, las=2)
text(-1,-10,"copies/mL", cex= 0.8,col="blue",xpd=TRUE)
text(-1,-6, texte52bis , cex= 0.7,col="black",xpd=TRUE)
}
pdf(file=figureExportee_Pdf, paper="a4r", height=9, width=8.5)
Standard_curves_copies_mL()
dev.off()
}else{}
}
}
Export_pdf.but <- tkbutton(fenetre_graphique, command=exporterpdfplot)
tkconfigure(Export_pdf.but,image=tkimage.create("photo",file=file.path(path.package("InterfaceqPCR"),"pdf.gif",
fsep=.Platform$file.sep)))
tkgrid(Export_pdf.but, row=4, column=2)
}
videregression <- tklabel(Interface_Total_qPCR, text=" ",font=fontHeading,foreground="chocolate4",bg="wheat1")
tkgrid(videregression, row=10, columnspan=4)
Calcul_regression.but <- tkbutton(Interface_Total_qPCR,command=Calcul_regression)
tkconfigure(Calcul_regression.but,image=tkimage.create("photo",file=file.path(path.package("InterfaceqPCR"),"calcul.gif",
fsep=.Platform$file.sep)))
tkgrid(Calcul_regression.but,row=11,column=2)
graphique_regression.but <- tkbutton(Interface_Total_qPCR,command=graphique_regression)
tkconfigure(graphique_regression.but,image=tkimage.create("photo",file=file.path(path.package("InterfaceqPCR"),"Plot.gif",
fsep=.Platform$file.sep)))
tkgrid(graphique_regression.but,row=11,column=3)
##############################################################################################
###############
vide3 <- tklabel(Interface_Total_qPCR, text="",font=fontHeading,foreground="chocolate4",bg="wheat1")
tkgrid(vide3, row=12, columnspan=4)
#etape3=tklabel(Interface_Total_qPCR, text="3 Concentration dans les \u00e9chantillons",font=fontHeading,foreground="chocolate4",bg="wheat1")
etape3 <- tklabel(Interface_Total_qPCR, text=texte29,font=fontHeading,foreground="chocolate4",bg="wheat1")
tkgrid(etape3, row=13, columnspan=6, sticky ="w")
#etape31=tklabel(Interface_Total_qPCR, text="Nb \u00e9chantillons",font=font2,foreground="chocolate4",bg="wheat1")
etape31 <- tklabel(Interface_Total_qPCR, text=texte61, font=font2,foreground="chocolate4",bg="wheat1")
tkgrid(etape31, row=14, column=2)
Calcul_Nb_echantillons =function(){
if(exists("dataimportees_echantillons")==FALSE) {" "} else {
Calcul_Nb_echantillons2=function(){
Nbechantillons <- subset(dataimportees_echantillons, ! Condition %in% c("PMA"))
Nbechantillons2 <- length(Nbechantillons$Nom_Echantillon)
Nbechantillons2 <<- as.character(Nbechantillons2)
}
}
}
ImportationNbFichier_ech_case <- tkentry(Interface_Total_qPCR,width=10,foreground=couleur1_ech,
bg="black", textvariable=tclVar(Calcul_Nb_echantillons()))
tkgrid(ImportationNbFichier_ech_case,row=14,column=3)
# R\u00e9cup\u00e9ration de l'\u00e9quation pour calculer les nombres de copies des \u00e9chantillons
## ATTENTION DONNEES EN LOG 10 PENSEZ A CONVERTIR
## La formule qui suit corrige le log10
calcul_echantillons <- function(){
regequation <- data.frame(summary(regressionnontraite)$coef[,1])
#row.names(regequation)=c("interception","pente")
row.names(regequation) <- c(texte30,texte31)
#colnames(regequation)=c("Valeurs")
colnames(regequation) <- c(texte32)
regequation <<- regequation
# R\u00e9cup\u00e9ration des Echantillons et Ct
# Subset garde uniquement les donn\u00e9es non traite au PMA
dataimportees_echantillons_nontraite <- subset(dataimportees_echantillons, ! Condition %in% c("PMA"))
Echantillons_bruts <- dataimportees_echantillons_nontraite
# Selection analyse UFC/mL ou nb copies/mL
# Condition permettant de v\u00e9rifier si la colonne Concentration UFC/mL existe
# Comme elle n'existe pas, elle se cr\u00e9\u00e9e
# Condition si anglais renomme les header colonnes
if(choixconcentration == texte52 ) {
if(exists("dataimportees_echantillons$Concentration_UFC_mL")==FALSE) {dataimportees_echantillons$Concentration_UFC_mL=0} else {dataimportees_echantillons$Concentration_UFC_mL}
Echantillons_bruts <<- Echantillons_bruts
Echantillons_bruts$Concentration_UFC_mL <- 10^((Echantillons_bruts$Ct-regequation[1,])/regequation[2,])
Echantillons_bruts <<- Echantillons_bruts
}else{
if(exists("dataimportees_echantillons$Concentration_copies_mL")==FALSE) {dataimportees_echantillons$Concentration_copies_mL=0} else {dataimportees_echantillons$Concentration_copies_mL}
Echantillons_bruts <<- Echantillons_bruts
Echantillons_bruts$Concentration_copies_mL <- 10^((Echantillons_bruts$Ct-regequation[1,])/regequation[2,])
Echantillons_bruts <<- Echantillons_bruts
}
# langue selectionnee : anglais
#if(choix_langue2 == "ANGLAIS" & choixconcentration == texte52) {
if(choix_langue == "ANGLAIS" & choixconcentration == texte52) {
names(Echantillons_bruts)[1] <- "Name_Sample"
names(Echantillons_bruts)[4] <- "Concentration_CFU_mL"
Echantillons_bruts <<- Echantillons_bruts
}else{}
#if(choix_langue2 == "ANGLAIS" & choixconcentration == texte53) {
if(choix_langue == "ANGLAIS" & choixconcentration == texte53) {
names(Echantillons_bruts)[1] <- "Name_Sample"
Echantillons_bruts <<- Echantillons_bruts
}else{}
}
Tableau_Echantillons_concentration <- function(){
## covert a data frame into a character based on
.toCharacter <- function(x,width,...) UseMethod(".toCharacter")
.toCharacter.default <- function(x,width,...) as.character(x)
.toCharacter.integer <- function(x,width,...) {
if(missing(width)) width <- max(nchar(as.character(x))) + 2
format(x, justify = "right", width = width)
}
.toCharacter.numeric <- function(x,width,...) {
if(missing(width)) width <- max(nchar(as.character(x))) + 2
format(x,trim = FALSE, width = width, justify = "right")
}
.toCharacter.factor <- function(x,width,...) {
if(missing(width)) width <- max(nchar(as.character(x))) + 2
.toCharacter(as.character(x),width,...)
}
.toCharacter.logical <- function(x,width,...) {
if(missing(width)) width <- 7
format(as.character(x), justify = "centre", width = width)
}
.toCharacter.data.frame <- function(x,width = 10, ...) {
nms <- dimnames(x)
DF <- as.data.frame(lapply(x,function(i) .toCharacter(i, width = width)),
stringsAsFactors = FALSE)
dimnames(DF) <- nms
return(DF)
}
addScrollbars <- function(parent, widget) {
xscr <- ttkscrollbar(parent, orient = "horizontal",
command = function(...) tkxview(widget, ...))
yscr <- ttkscrollbar(parent, orient = "vertical",
command = function(...) tkyview(widget, ...))
tkconfigure(widget,
xscrollcommand = function(...) tkset(xscr,...),
yscrollcommand = function(...) tkset(yscr,...))
tkgrid(widget, row = 0, column = 0, sticky = "news")
tkgrid(yscr,row = 0,column = 1, sticky = "ns")
tkgrid(xscr, row = 1, column = 0, sticky = "ew")
tkgrid.columnconfigure(parent, 0, weight = 1)
tkgrid.rowconfigure(parent, 0, weight = 1)
}
affichage_concentration_Echantillons <<- Echantillons_bruts
affichage_concentration_Echantillons[,1] <- as.character(Echantillons_bruts[,1])
affichage_concentration_Echantillons[,2] <- as.character(Echantillons_bruts[,2])
affichage_concentration_Echantillons[,3] <- as.numeric(Echantillons_bruts[,3])
affichage_concentration_Echantillons[,4] <- as.numeric(Echantillons_bruts[,4])
DF <- affichage_concentration_Echantillons
###################################################
window_affichage_concentration_Echantillons <- tktoplevel()
#tkwm.title(window_affichage_concentration_Echantillons, "R\u00e9sultats des qPCR")
tkwm.title(window_affichage_concentration_Echantillons, texte33bis)
tkwm.geometry(window_affichage_concentration_Echantillons, "600x450")
frame <- ttkframe(window_affichage_concentration_Echantillons, padding = c(3,3,3,12))
tkpack(frame, expand = TRUE, fill = "both")
###################################################
frame_0 <- ttkframe(frame); tkpack(frame_0, fill = "x")
#label <- ttklabel(frame_0, text = "filtre:")
label <- ttklabel(frame_0, text = texte34)
tkpack(label, side = "left")
filter_var <- tclVar("")
filter_entry <- ttkentry(frame_0, textvariable = filter_var)
tkpack(filter_entry, side = "left")
###################################################
frame_1 <- ttkframe(frame)
tkpack(frame_1, expand = TRUE, fill = "both")
treeview <- ttktreeview(frame_1, columns = 1:ncol(DF),
#displaycolumns = 1:ncol(DF),
show = "headings", # not "tree"
selectmode = "browse") # single selection
addScrollbars(frame_1, treeview)
frame_2 <- ttkframe(frame); tkpack(frame_2, fill = "both")
Savefunctioncsv <- function(){
#### Select field to import ASCII profiles ####
#fil=if (interactive()) file.choose()
tt2 <- tktoplevel()
tkwm.geometry(tt2, "400x200")
#tkwm.title(tt2,"Exporter fichier.csv")
tkwm.title(tt2, texte35)
tkgrid(tklabel(tt2,text=""))
t1 <- tkframe(tt2)
#text1<-tklabel(t1,text="Quel est le s\u00e9parateur ?")
text1 <- tklabel(t1,text=texte36)
#sep1<-c("tab (tabulation)",", (virgule)","; (point virgule)",". (point)"," (espace)")
sep1 <- c(texte37,texte13,texte38,texte12,texte39)
sep2 <- tkwidget(t1,"ComboBox",editable=FALSE,values=sep1,height=3)
tkpack(text1,sep2,side="left")
tkgrid(t1)
t2 <- tkframe(tt2)
#text2<-tklabel(t2,text="Quel est le symbole d\u00e9cimal ?")
text2 <- tklabel(t2,text=texte11)
#dec1<-c(". (point)",", (virgule)")
dec1 <- c(texte12,texte13)
dec2 <- tkwidget(t2,"ComboBox",editable=FALSE,values=dec1,height=2)
tkpack(text2,dec2,side="left")
tkgrid(t2)
#t3<-tkframe(tt2)
#text3<-tklabel(t3,text="Do you have header")
#hea1 <- c("yes","no")
#hea2 <- tkwidget(t3,"ComboBox",editable=FALSE,values=hea1,height=2)
#tkpack(text3,hea2,side="left")
#tkgrid(t3)
tkgrid(tklabel(tt2,text=""))
#### Preview channels ####
view.channels <- function()
{
sep3 <-unlist(as.numeric(tcl(sep2,"getvalue"))+1 )
if(sep3==1) sep4 <- "\t"
if(sep3==2) sep4 <- ","
if(sep3==3) sep4 <- ";"
if(sep3==4) sep4 <- "."
if(sep3==5) sep4 <- " "
dec3 <-unlist(as.numeric(tcl(dec2,"getvalue"))+1 )
if(dec3==1) dec4 <- "."
if(dec3==2) dec4 <- ","
#hea3 <-unlist(as.numeric(tcl(hea2,"getvalue"))+1 )
#if(hea3==1) hea4<-TRUE
#if(hea3==2) hea4<-FALSE
dataExportees <- tclvalue(tkgetSaveFile())
dataexportees <- paste(dataExportees,".csv",sep="")
write.table(affichage_concentration_Echantillons,file = dataexportees,col.names=T,row.names=F,dec=dec4,sep=sep4)
tkdestroy(tt2)
}
#tkgrid(tkbutton(tt2,text="Exporter fichier",command=view.channels))
tkgrid(tkbutton(tt2,text=texte40,command=view.channels))
tkgrid(tklabel(tt2,text=""))
}
#Savecsv.but<-tkbutton(frame_2,text=" Exporter\ncsv ",command=Savefunctioncsv)
Savecsv.but <- tkbutton(frame_2,text=texte41,command=Savefunctioncsv)
tkgrid(Savecsv.but,row=1,column=2)
Savefunctionxlsx <- function(){
#Exportationfichierxlsx=tkmessageBox(title="Exporter fichier en xlsx", message=" Voulez-vous exporter votre fichier en xlsx ?",
# icon="info",type="yesno")
Exportationfichierxlsx <- tkmessageBox(title=texte42, message=texte43,
icon="info",type="yesno")
Exportationfichierxlsx1 <- tclvalue(Exportationfichierxlsx)
if(Exportationfichierxlsx1=="yes") {
dataExportees <- tclvalue(tkgetSaveFile())
dataexportees <- paste(dataExportees,".xlsx",sep="")
write.xlsx(affichage_concentration_Echantillons,file = dataexportees,col.names=T,row.names=F,sheetName="1")
}else{tkdestroy(Exportationfichierxlsx)}
}
#Savexlsx.but<-tkbutton(frame_2,text=" Exporter\nxlsx ",command=Savefunctionxlsx)
Savexlsx.but <- tkbutton(frame_2,text= texte44,command=Savefunctionxlsx)
tkgrid(Savexlsx.but,row=1,column=4)
###################################################
widths <- c(rep(100,dim(DF)[2])) #c(100,200) #rep(100,dim(DF)[2])) # hard coded
nms <- names(DF)
for(i in 1:dim(DF)[2]) {
tcl(treeview, "heading", i, text = nms[i])
tcl(treeview, "column", i, width = widths[i],
stretch = TRUE, anchor = "w")
}
###################################################
fillTable <- function(treeview, DF) {
children <- as.character(tcl(treeview, "children", ""))
for(i in children)
tcl(treeview, "delete", i)
#shade <- c("none", "gray")
for(i in seq_len(nrow(DF)))
tcl(treeview, "insert", "", "end",
text = "",
values = unlist(DF[i,]))
tktag.configure(treeview, "gray", background = "red")
}
###################################################
fillTable(treeview, DF)
## permet utiliser la commade filtre
cur_ind <- 1:nrow(DF)
tkbind(filter_entry, "<KeyRelease>", function(W, K) {
val <- tclvalue(tkget(W))
poss_vals <- apply(DF, 1, function(...)
paste(..., collapse = " "))
ind<- grep(val, poss_vals)
if(length(ind) == 0) ind <- 1:nrow(DF)
fillTable(treeview, DF[ind,])
})
} # fin de la function table
Calulechantillons_et_tableau_resultats <- function(){
calcul_echantillons()
Tableau_Echantillons_concentration()
}
Calcul_echantillons.but <- tkbutton(Interface_Total_qPCR,command=Calulechantillons_et_tableau_resultats)
tkconfigure(Calcul_echantillons.but,image=tkimage.create("photo",file=file.path(path.package("InterfaceqPCR"),"Tubes.gif",
fsep=.Platform$file.sep)))
tkgrid(Calcul_echantillons.but,row=15,column=3, columnspan=3)
##########################################################################################################
######
apropos <- function(){
aidefenetre <- tktoplevel()
#tkwm.title(aidefenetre," A propos de InterfaceqPCR")
tkwm.title(aidefenetre,texte6)
tkconfigure(aidefenetre,bg="gray80",cursor="hand2") # wheat1 hand2
# Taille
tkwm.geometry(aidefenetre, "500x600") # Largueur x hauteur
tkwm.resizable(aidefenetre,F,F)
# Police
font2 <- tkfont.create(family="times",size=14,weight="bold",slant="italic")
font3 <- tkfont.create(family="times",size=12,weight="bold")
path.logobatman <- file.path(path.package("InterfaceqPCR"),"a_laise_BZH2.gif", fsep=.Platform$file.sep)
mon.imagebatman <- tkimage.create("photo", file=path.logobatman )
montre.batman <- tklabel(aidefenetre, image=mon.imagebatman, background="white")
tkgrid(montre.batman,row=1, column=3,columnspan=2)
videaide <- tklabel(aidefenetre,text=" ",font=font2,bg="gray80")
tkgrid(videaide,row=2)
# message<-tklabel(aidefenetre,text="InterfaceqPCR\nTraitement des donn\u00e9es issues de la qPCR Version 1.0
# \nOlivier Le Goff
# \nLaboratoire EA CIDAM Clermont-Ferrand\nUniversit\u00e9 d'Auvergne\n2016",bg="gray80",font=font3)
#
message <- tklabel(aidefenetre,text=texte7,bg="gray80",font=font3)
tkgrid(message,row=3, column=3,columnspan=2)
path.logoimmunoaide <- file.path(path.package("InterfaceqPCR"),"logoEAUDA.gif", fsep=.Platform$file.sep)
mon.imageimmunoaide <- tkimage.create("photo", file=path.logoimmunoaide)
montre.imageimmunoaide <- tklabel(aidefenetre, image=mon.imageimmunoaide, background="white")
tkgrid(montre.imageimmunoaide,row=4, column=3)
fermeraide=function(){
tkdestroy(aidefenetre)
}
#Ok.butaide<-tkbutton(aidefenetre,text="Quitter",command=fermeraide,font=font2,foreground="Blue")
Ok.butaide <- tkbutton(aidefenetre,text=texte8, command=fermeraide,font=font2,foreground="Blue")
tkgrid(Ok.butaide,row=4, column=4)
}
fermeture_Interface_qPCR=function(){
tkdestroy(Interface_Total_qPCR)
Interface_qPCR_choix()
}
Fermeture_qPCR.but <- tkbutton(Interface_Total_qPCR,command=fermeture_Interface_qPCR)
tkconfigure(Fermeture_qPCR.but,image=tkimage.create("photo",file=file.path(path.package("InterfaceqPCR"),"start.gif",
fsep=.Platform$file.sep)))
tkgrid(Fermeture_qPCR.but,row=16,column=2)
Aide.but <- tkbutton(Interface_Total_qPCR,command=apropos)
tkconfigure(Aide.but,image=tkimage.create("photo",file=file.path(path.package("InterfaceqPCR"),"apropos.gif",
fsep=.Platform$file.sep)))
tkgrid(Aide.but,row=16,column=7)
} # fin de la fonction Interface_qPCR
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