Nothing
inst/extdata/agtwo2.R
In maGUI: A Graphical User Interface for Microarray Data Analysis and Annotation
agtwo<-function(h,...){
folder<-tclvalue(tkchooseDirectory(title="Select the folder"))
tag2_i<<-tag2_i+1
folder_Ag2[[tag2_i]]<<-folder
if(folder_Ag2[[tag2_i]]==""){
folder_Ag2<-NULL
} else {
try(({
pb_ma<-tkProgressBar(title="Pre-processing...",label="",min=0,max=1,initial=0,width=500)
setTkProgressBar(pb_ma,0.3,title=NULL,label="")
new_datAgTwo=NULL
setwd(folder_Ag2[[tag2_i]])
new_datAgTwo<-read.maimages(files=dir(folder_Ag2[[tag2_i]]),source="agilent")
if(length(new_datAgTwo)!=0){datAgTwo=NULL;datAgTwo<-new_datAgTwo}
setTkProgressBar(pb_ma,0.7,title=NULL,label="")
z<-as(datAgTwo,"NChannelSet")
ann_Ag2[[tag2_i]]<<-annotation(z)
}),silent=TRUE)
setTkProgressBar(pb_ma,1,title="Completed...",label="")
close(pb_ma)
if(length(new_datAgTwo)==0)tkmessageBox(title="Error",message="Could not load this type of data! Try Series_matrix or Online_Data",icon="error",type="ok")
}
if(length(datAgTwo)!=0){
if(length(new_datAgTwo)!=0){
prnt<-paste("Agilent-TwoColor",tag2_i,sep="_")
tree_prnts<<-c(tree_prnts,prnt)
l_datAgTwo[[tag2_i]]<<-datAgTwo
p_enter<-tcl(treeview,"insert","","end",values=as.tclObj(prnt))
autopa<-tkmessageBox(title="Confirm",message="Do you want to pre-process and analyze automatically!",icon="question",type="okcancel")
if(tclvalue(autopa)=="ok"){
pb_ma<-tkProgressBar(title="Normalization...",label="",min=0,max=1,initial=0,width=500)
datAgTwo2.m=NULL;use.datAgTwo2.m=NULL;xf=NULL;datAgTwo2.f=NULL;datAgTwo2.s=NULL;
design=NULL;design_Ag2=NULL;ttx=NULL;DE_Ag2=NULL;DE_Ag2_2=NULL;use_DE_Ag2=NULL;
sample.dist_Ag2=NULL;
# pca_Ag2=NULL;
# sample.clust_Ag2=NULL;
# clas_Ag2=NULL;
try(({folder_Ag2[[tag2_i]]<-folder_Ag2[[tag2_i]];datAgTwo<-datAgTwo;heatcol<-heatcol; }),silent=TRUE)
setwd(folder_Ag2[[tag2_i]])
setTkProgressBar(pb_ma,0.1,title=NULL,label="")
try(datAgTwo2<-backgroundCorrect(datAgTwo,"normexp"),silent=TRUE)
if(length(datAgTwo2)==0)datAgTwo2<-datAgTwo
datAgTwo2<-normalizeBetweenArrays(datAgTwo2$R,method="quantile")
datAgTwo2<-log(datAgTwo2)
datAgTwo2.m<-datAgTwo2
datAgTwo2.m<-as.matrix(datAgTwo2.m)
try({
if(length(rownames(datAgTwo2.m))==0){
rownames(datAgTwo2.m)<-1:length(datAgTwo2.m[,1])
} else {
rownames(datAgTwo2.m)<-as.character(rownames(datAgTwo2.m))
}
},silent=TRUE)
ta_ag2_norm=NULL
ta_ag2_norm<-tclArray()
for(i in 0:dim(datAgTwo2.m)[1]){ for(j in 0:dim(datAgTwo2.m)[2]){
if(i==0){ ta_ag2_norm[[i,j]]<-colnames(datAgTwo2.m)[j] } else {
if(j==0){ ta_ag2_norm[[i,j]]<-rownames(datAgTwo2.m)[i] } else {
tem<-datAgTwo2.m[i,j]
ta_ag2_norm[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
} }
} }
# datAgTwo2.m[[tag2_i]]<<-datAgTwo2.m[[tag2_i]]
datAgTwo2.m2[[tag2_i]]<<-datAgTwo2.m
ta_ag2_norm2[[tag2_i]]<<-ta_ag2_norm
#
p_enter_norm<-tcl(treeview,"insert",p_enter,"end",values=as.tclObj("...Normalization"))
setTkProgressBar(pb_ma,0.3,title="QC...",label="")
if(is.null(ma_img)==TRUE){
try(tkpack.forget(tableData,scrX,scrY),silent=TRUE)
try(tkwm.withdraw(w_legend),silent=TRUE)
ma_img<<-tkrplot(getToolkitWidget(ma_frame2),function(...){boxplot(datAgTwo2.m2[[tag2_i]])},hscale=1.7,vscale=1.07)
ma_img2<<-ma_img
tkpack(ma_img2)
} else {
ma_img2<<-tkrreplot(ma_img,function(...){boxplot(datAgTwo2.m2[[tag2_i]])},hscale=1.7,vscale=1.07)
}
p_enter_qc<-tcl(treeview,"insert",p_enter,"end",values=as.tclObj("...QC"))
setTkProgressBar(pb_ma,0.35,title="Filtering...",label="")
use.datAgTwo2.m<-datAgTwo2.m
try(({
fff<-pOverA(A=1,p=0.05)
i<-genefilter(use.datAgTwo2.m,fff)
dat.fo<-use.datAgTwo2.m[i,]
i<-genefilter(-use.datAgTwo2.m,fff)
dat.fu<-use.datAgTwo2.m[i,]
dat.f<-unique(rbind(dat.fo,dat.fu))
fit<-lmFit(dat.f)
fit2<-eBayes(fit)
fit2_Ag2[[tag2_i]]<<-fit2
datAgTwo2.f<-fit2
}),silent=TRUE)
if(length(datAgTwo2.f)==0)
{
try(({
rsd<-rowSds(use.datAgTwo2.m)
i<-rsd>=2
dat.f<-use.datAgTwo2.m[i,]
fit<-lmFit(dat.f)
fit2<-eBayes(fit)
fit2_Ag2[[tag2_i]]<<-fit2
datAgTwo2.f<-fit2
}),silent=TRUE)
}
ps1<-as.data.frame(datAgTwo2.f)
rownames(ps1)<-rownames(datAgTwo2.f)
datAgTwo2.f2=NULL
datAgTwo2.f2<-ps1
ta_ag2_filt=NULL
ta_ag2_filt<-tclArray()
for(i in 0:dim(datAgTwo2.f2)[1]){ for(j in 0:dim(datAgTwo2.f2)[2]){
if(i==0){ ta_ag2_filt[[i,j]]<-colnames(datAgTwo2.f2)[j] } else {
if(j==0){ ta_ag2_filt[[i,j]]<-rownames(datAgTwo2.f2)[i] } else {
tem<-datAgTwo2.f2[i,j]
ta_ag2_filt[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
} }
} }
datAgTwo2.f3[[tag2_i]]<<-datAgTwo2.f2
ta_ag2_filt2[[tag2_i]]<<-ta_ag2_filt
p_enter_filter<-tcl(treeview,"insert",p_enter,"end",values=as.tclObj("...Filtering"))
setTkProgressBar(pb_ma,0.55,title="Statistical_Significant...",label="")
if(length(datAgTwo2.f)!=0){
err<-try({
ttx<-topTable(datAgTwo2.f,number=nrow(use.datAgTwo2.m))
rn<-rownames(ttx)[which(rownames(ttx)%in%rownames(datAgTwo2.m)==TRUE)]
datAgTwo2.s<-use.datAgTwo2.m[rn,]
},silent=TRUE)
if(length(grep("Error",err))!=0)
{
ttx<-topTable(datAgTwo2.f,number=nrow(use.datAgTwo2.m))
rn<-as.numeric(rownames(ttx)[which(rownames(ttx)%in%rownames(datAgTwo2.m)==TRUE)])
datAgTwo2.s<-datAgTwo2.m[rownames(ttx)[ttx$P.Value<=0.01],]
}
}
datAgTwo2.s2=NULL
datAgTwo2.s2<-datAgTwo2.s
ta_ag2_stat=NULL
ta_ag2_stat<-tclArray()
for(i in 0:dim(datAgTwo2.s2)[1]){ for(j in 0:dim(datAgTwo2.s2)[2]){
if(i==0){ ta_ag2_stat[[i,j]]<-colnames(datAgTwo2.s2)[j] } else {
if(j==0){ ta_ag2_stat[[i,j]]<-rownames(datAgTwo2.s2)[i] } else {
tem<-datAgTwo2.s2[i,j]
ta_ag2_stat[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
} }
} }
datAgTwo2.s3[[tag2_i]]<<-datAgTwo2.s2
ta_ag2_stat2[[tag2_i]]<<-ta_ag2_stat
p_enter_stat_sign<-tcl(treeview,"insert",p_enter,"end",values=as.tclObj("...Statistical_Significant"))
setTkProgressBar(pb_ma,0.75,title="DGE...",label="")
err<-try(DE_Ag2<-topTable(datAgTwo2.f),silent=TRUE)
err<-try(DE_Ag2All[[tag2_i]]<<-topTable(datAgTwo2.f,number=nrow(datAgTwo2.f)),silent=TRUE)
ta_ag2_dge=NULL
ta_ag2_dge<-tclArray()
for(i in 0:dim(DE_Ag2)[1]){ for(j in 0:dim(DE_Ag2)[2]){
if(i==0){ ta_ag2_dge[[i,j]]<-colnames(DE_Ag2)[j] } else {
if(j==0){ ta_ag2_dge[[i,j]]<-rownames(DE_Ag2)[i] } else {
tem<-DE_Ag2[i,j]
ta_ag2_dge[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
} }
} }
DE_Ag2_2[[tag2_i]]<<-DE_Ag2
ta_ag2_dge2[[tag2_i]]<<-ta_ag2_dge
p_enter_dge<-tcl(treeview,"insert",p_enter,"end",values=as.tclObj("...DGE"))
setTkProgressBar(pb_ma,0.85,title="PCA...",label="")
pca_Ag2[[tag2_i]]<<-prcomp(t(datAgTwo2.m))
if(is.null(ma_img)==TRUE){
try(tkpack.forget(tableData,scrX,scrY),silent=TRUE)
try(tkwm.withdraw(w_legend),silent=TRUE)
ma_img<<-tkrplot(getToolkitWidget(ma_frame2),function(...){plot(pca_Ag2[[tag2_i]])},hscale=1.7,vscale=1.07)
ma_img2<<-ma_img
tkpack(ma_img2)
} else {
ma_img2<<-tkrreplot(ma_img,function(...){plot(pca_Ag2[[tag2_i]])},hscale=1.7,vscale=1.07)
}
p_enter_pca<-tcl(treeview,"insert",p_enter,"end",values=as.tclObj("...PCA"))
setTkProgressBar(pb_ma,0.9,title="Clustering...",label="")
sample.dist_c1<-dist(t(datAgTwo2.m))
sample.dist_Ag2<-as.dist(1-cor(datAgTwo2.m,method="pearson"))
sample.clust_Ag2[[tag2_i]]<<-hclust(sample.dist_Ag2,method="complete")
if(is.null(ma_img)==TRUE){
try(tkpack.forget(tableData,scrX,scrY),silent=TRUE)
try(tkwm.withdraw(w_legend),silent=TRUE)
ma_img<<-tkrplot(getToolkitWidget(ma_frame2),function(...){plot(sample.clust_Ag2[[tag2_i]])},hscale=1.7,vscale=1.07)
ma_img2<<-ma_img
tkpack(ma_img2)
}else{
ma_img2<<-tkrreplot(ma_img,function(...){plot(sample.clust_Ag2[[tag2_i]])},hscale=1.7,vscale=1.07)
}
p_enter_clust<-tcl(treeview,"insert",p_enter,"end",values=as.tclObj("...Clustering"))
setTkProgressBar(pb_ma,0.95,title="Classification...",label="")
er_x<-try(use_DE_Ag2<-as.matrix(DE_Ag2),silent=TRUE)
if(length(grep("Error",er_x))!=0)
{
rownames(DE_Ag2)<-as.character(DE_Ag2)
use_DE_Ag2<-as.matrix(DE_Ag2)
}
rnames<-rownames(use_DE_Ag2)
clas_Ag2[[tag2_i]]<<-as.matrix(use.datAgTwo2.m[rnames,])
if(is.null(ma_img)==TRUE){
try(tkpack.forget(tableData,scrX,scrY),silent=TRUE)
try(tkwm.withdraw(w_legend),silent=TRUE)
ma_img<<-tkrplot(getToolkitWidget(ma_frame2),function(...){
heatmap(clas_Ag2[[tag2_i]],Rowv=NA,Colv=NA,cexCol=0.8,cexRow=0.8,col=heatcol)
},hscale=1.7,vscale=1.07)
ma_img2<<-ma_img
tkpack(ma_img2)
}else{
ma_img2<<-tkrreplot(ma_img,function(...){
heatmap(clas_Ag2[[tag2_i]],Rowv=NA,Colv=NA,cexCol=0.8,cexRow=0.8,col=heatcol)
},hscale=1.7,vscale=1.07)
}
p_enter_class<-tcl(treeview,"insert",p_enter,"end",values=as.tclObj("...Classification"))
setTkProgressBar(pb_ma,1,title="Completed...",label="")
close(pb_ma)
}
}
}
display()
}
pb_ma<-tkProgressBar(title="Loading packages...",label="",min=0,max=1,initial=0,width=500)
setTkProgressBar(pb_ma,0.2,title=NULL,label="")
if(!requireNamespace("gWidgets2tcltk",quietly=TRUE)){install.packages("gWidgets2tcltk");library(gWidgets2tcltk)} else {library(gWidgets2tcltk)}
setTkProgressBar(pb_ma,0.3,title=NULL,label="")
if(!requireNamespace("tkrplot",quietly=TRUE)){install.packages("tkrplot");library(tkrplot)} else {library(tkrplot)}
setTkProgressBar(pb_ma,0.4,title=NULL,label="")
if(!requireNamespace("BiocManager",quietly=TRUE)){install.packages("BiocManager");library(BiocManager)} else {library(BiocManager)}
setTkProgressBar(pb_ma,0.6,title=NULL,label="")
if(!requireNamespace("genefilter",quietly=TRUE)){BiocManager::install("genefilter",ask=FALSE,update=FALSE);library(genefilter)} else {library(genefilter)}
setTkProgressBar(pb_ma,0.7,title=NULL,label="")
if(!requireNamespace("limma",quietly=TRUE)){BiocManager::install("limma",ask=FALSE,update=FALSE);library(limma)} else {library(limma)}
setTkProgressBar(pb_ma,0.8,title=NULL,label="")
if(!requireNamespace("stats",quietly=TRUE)){install.packages("stats",ask=FALSE,update=FALSE);library(stats)} else {library(stats)}
setTkProgressBar(pb_ma,0.9,title=NULL,label="")
if(!requireNamespace("tcltk",quietly=TRUE)){install.packages("tcltk",ask=FALSE,update=FALSE);library(tcltk)} else {library(tcltk)}
setTkProgressBar(pb_ma,1,title="Done...",label="")
close(pb_ma)
agtwo()
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agtwo<-function(h,...){
folder<-tclvalue(tkchooseDirectory(title="Select the folder"))
tag2_i<<-tag2_i+1
folder_Ag2[[tag2_i]]<<-folder
if(folder_Ag2[[tag2_i]]==""){
folder_Ag2<-NULL
} else {
try(({
pb_ma<-tkProgressBar(title="Pre-processing...",label="",min=0,max=1,initial=0,width=500)
setTkProgressBar(pb_ma,0.3,title=NULL,label="")
new_datAgTwo=NULL
setwd(folder_Ag2[[tag2_i]])
new_datAgTwo<-read.maimages(files=dir(folder_Ag2[[tag2_i]]),source="agilent")
if(length(new_datAgTwo)!=0){datAgTwo=NULL;datAgTwo<-new_datAgTwo}
setTkProgressBar(pb_ma,0.7,title=NULL,label="")
z<-as(datAgTwo,"NChannelSet")
ann_Ag2[[tag2_i]]<<-annotation(z)
}),silent=TRUE)
setTkProgressBar(pb_ma,1,title="Completed...",label="")
close(pb_ma)
if(length(new_datAgTwo)==0)tkmessageBox(title="Error",message="Could not load this type of data! Try Series_matrix or Online_Data",icon="error",type="ok")
}
if(length(datAgTwo)!=0){
if(length(new_datAgTwo)!=0){
prnt<-paste("Agilent-TwoColor",tag2_i,sep="_")
tree_prnts<<-c(tree_prnts,prnt)
l_datAgTwo[[tag2_i]]<<-datAgTwo
p_enter<-tcl(treeview,"insert","","end",values=as.tclObj(prnt))
autopa<-tkmessageBox(title="Confirm",message="Do you want to pre-process and analyze automatically!",icon="question",type="okcancel")
if(tclvalue(autopa)=="ok"){
pb_ma<-tkProgressBar(title="Normalization...",label="",min=0,max=1,initial=0,width=500)
datAgTwo2.m=NULL;use.datAgTwo2.m=NULL;xf=NULL;datAgTwo2.f=NULL;datAgTwo2.s=NULL;
design=NULL;design_Ag2=NULL;ttx=NULL;DE_Ag2=NULL;DE_Ag2_2=NULL;use_DE_Ag2=NULL;
sample.dist_Ag2=NULL;
# pca_Ag2=NULL;
# sample.clust_Ag2=NULL;
# clas_Ag2=NULL;
try(({folder_Ag2[[tag2_i]]<-folder_Ag2[[tag2_i]];datAgTwo<-datAgTwo;heatcol<-heatcol; }),silent=TRUE)
setwd(folder_Ag2[[tag2_i]])
setTkProgressBar(pb_ma,0.1,title=NULL,label="")
try(datAgTwo2<-backgroundCorrect(datAgTwo,"normexp"),silent=TRUE)
if(length(datAgTwo2)==0)datAgTwo2<-datAgTwo
datAgTwo2<-normalizeBetweenArrays(datAgTwo2$R,method="quantile")
datAgTwo2<-log(datAgTwo2)
datAgTwo2.m<-datAgTwo2
datAgTwo2.m<-as.matrix(datAgTwo2.m)
try({
if(length(rownames(datAgTwo2.m))==0){
rownames(datAgTwo2.m)<-1:length(datAgTwo2.m[,1])
} else {
rownames(datAgTwo2.m)<-as.character(rownames(datAgTwo2.m))
}
},silent=TRUE)
ta_ag2_norm=NULL
ta_ag2_norm<-tclArray()
for(i in 0:dim(datAgTwo2.m)[1]){ for(j in 0:dim(datAgTwo2.m)[2]){
if(i==0){ ta_ag2_norm[[i,j]]<-colnames(datAgTwo2.m)[j] } else {
if(j==0){ ta_ag2_norm[[i,j]]<-rownames(datAgTwo2.m)[i] } else {
tem<-datAgTwo2.m[i,j]
ta_ag2_norm[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
} }
} }
# datAgTwo2.m[[tag2_i]]<<-datAgTwo2.m[[tag2_i]]
datAgTwo2.m2[[tag2_i]]<<-datAgTwo2.m
ta_ag2_norm2[[tag2_i]]<<-ta_ag2_norm
#
p_enter_norm<-tcl(treeview,"insert",p_enter,"end",values=as.tclObj("...Normalization"))
setTkProgressBar(pb_ma,0.3,title="QC...",label="")
if(is.null(ma_img)==TRUE){
try(tkpack.forget(tableData,scrX,scrY),silent=TRUE)
try(tkwm.withdraw(w_legend),silent=TRUE)
ma_img<<-tkrplot(getToolkitWidget(ma_frame2),function(...){boxplot(datAgTwo2.m2[[tag2_i]])},hscale=1.7,vscale=1.07)
ma_img2<<-ma_img
tkpack(ma_img2)
} else {
ma_img2<<-tkrreplot(ma_img,function(...){boxplot(datAgTwo2.m2[[tag2_i]])},hscale=1.7,vscale=1.07)
}
p_enter_qc<-tcl(treeview,"insert",p_enter,"end",values=as.tclObj("...QC"))
setTkProgressBar(pb_ma,0.35,title="Filtering...",label="")
use.datAgTwo2.m<-datAgTwo2.m
try(({
fff<-pOverA(A=1,p=0.05)
i<-genefilter(use.datAgTwo2.m,fff)
dat.fo<-use.datAgTwo2.m[i,]
i<-genefilter(-use.datAgTwo2.m,fff)
dat.fu<-use.datAgTwo2.m[i,]
dat.f<-unique(rbind(dat.fo,dat.fu))
fit<-lmFit(dat.f)
fit2<-eBayes(fit)
fit2_Ag2[[tag2_i]]<<-fit2
datAgTwo2.f<-fit2
}),silent=TRUE)
if(length(datAgTwo2.f)==0)
{
try(({
rsd<-rowSds(use.datAgTwo2.m)
i<-rsd>=2
dat.f<-use.datAgTwo2.m[i,]
fit<-lmFit(dat.f)
fit2<-eBayes(fit)
fit2_Ag2[[tag2_i]]<<-fit2
datAgTwo2.f<-fit2
}),silent=TRUE)
}
ps1<-as.data.frame(datAgTwo2.f)
rownames(ps1)<-rownames(datAgTwo2.f)
datAgTwo2.f2=NULL
datAgTwo2.f2<-ps1
ta_ag2_filt=NULL
ta_ag2_filt<-tclArray()
for(i in 0:dim(datAgTwo2.f2)[1]){ for(j in 0:dim(datAgTwo2.f2)[2]){
if(i==0){ ta_ag2_filt[[i,j]]<-colnames(datAgTwo2.f2)[j] } else {
if(j==0){ ta_ag2_filt[[i,j]]<-rownames(datAgTwo2.f2)[i] } else {
tem<-datAgTwo2.f2[i,j]
ta_ag2_filt[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
} }
} }
datAgTwo2.f3[[tag2_i]]<<-datAgTwo2.f2
ta_ag2_filt2[[tag2_i]]<<-ta_ag2_filt
p_enter_filter<-tcl(treeview,"insert",p_enter,"end",values=as.tclObj("...Filtering"))
setTkProgressBar(pb_ma,0.55,title="Statistical_Significant...",label="")
if(length(datAgTwo2.f)!=0){
err<-try({
ttx<-topTable(datAgTwo2.f,number=nrow(use.datAgTwo2.m))
rn<-rownames(ttx)[which(rownames(ttx)%in%rownames(datAgTwo2.m)==TRUE)]
datAgTwo2.s<-use.datAgTwo2.m[rn,]
},silent=TRUE)
if(length(grep("Error",err))!=0)
{
ttx<-topTable(datAgTwo2.f,number=nrow(use.datAgTwo2.m))
rn<-as.numeric(rownames(ttx)[which(rownames(ttx)%in%rownames(datAgTwo2.m)==TRUE)])
datAgTwo2.s<-datAgTwo2.m[rownames(ttx)[ttx$P.Value<=0.01],]
}
}
datAgTwo2.s2=NULL
datAgTwo2.s2<-datAgTwo2.s
ta_ag2_stat=NULL
ta_ag2_stat<-tclArray()
for(i in 0:dim(datAgTwo2.s2)[1]){ for(j in 0:dim(datAgTwo2.s2)[2]){
if(i==0){ ta_ag2_stat[[i,j]]<-colnames(datAgTwo2.s2)[j] } else {
if(j==0){ ta_ag2_stat[[i,j]]<-rownames(datAgTwo2.s2)[i] } else {
tem<-datAgTwo2.s2[i,j]
ta_ag2_stat[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
} }
} }
datAgTwo2.s3[[tag2_i]]<<-datAgTwo2.s2
ta_ag2_stat2[[tag2_i]]<<-ta_ag2_stat
p_enter_stat_sign<-tcl(treeview,"insert",p_enter,"end",values=as.tclObj("...Statistical_Significant"))
setTkProgressBar(pb_ma,0.75,title="DGE...",label="")
err<-try(DE_Ag2<-topTable(datAgTwo2.f),silent=TRUE)
err<-try(DE_Ag2All[[tag2_i]]<<-topTable(datAgTwo2.f,number=nrow(datAgTwo2.f)),silent=TRUE)
ta_ag2_dge=NULL
ta_ag2_dge<-tclArray()
for(i in 0:dim(DE_Ag2)[1]){ for(j in 0:dim(DE_Ag2)[2]){
if(i==0){ ta_ag2_dge[[i,j]]<-colnames(DE_Ag2)[j] } else {
if(j==0){ ta_ag2_dge[[i,j]]<-rownames(DE_Ag2)[i] } else {
tem<-DE_Ag2[i,j]
ta_ag2_dge[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
} }
} }
DE_Ag2_2[[tag2_i]]<<-DE_Ag2
ta_ag2_dge2[[tag2_i]]<<-ta_ag2_dge
p_enter_dge<-tcl(treeview,"insert",p_enter,"end",values=as.tclObj("...DGE"))
setTkProgressBar(pb_ma,0.85,title="PCA...",label="")
pca_Ag2[[tag2_i]]<<-prcomp(t(datAgTwo2.m))
if(is.null(ma_img)==TRUE){
try(tkpack.forget(tableData,scrX,scrY),silent=TRUE)
try(tkwm.withdraw(w_legend),silent=TRUE)
ma_img<<-tkrplot(getToolkitWidget(ma_frame2),function(...){plot(pca_Ag2[[tag2_i]])},hscale=1.7,vscale=1.07)
ma_img2<<-ma_img
tkpack(ma_img2)
} else {
ma_img2<<-tkrreplot(ma_img,function(...){plot(pca_Ag2[[tag2_i]])},hscale=1.7,vscale=1.07)
}
p_enter_pca<-tcl(treeview,"insert",p_enter,"end",values=as.tclObj("...PCA"))
setTkProgressBar(pb_ma,0.9,title="Clustering...",label="")
sample.dist_c1<-dist(t(datAgTwo2.m))
sample.dist_Ag2<-as.dist(1-cor(datAgTwo2.m,method="pearson"))
sample.clust_Ag2[[tag2_i]]<<-hclust(sample.dist_Ag2,method="complete")
if(is.null(ma_img)==TRUE){
try(tkpack.forget(tableData,scrX,scrY),silent=TRUE)
try(tkwm.withdraw(w_legend),silent=TRUE)
ma_img<<-tkrplot(getToolkitWidget(ma_frame2),function(...){plot(sample.clust_Ag2[[tag2_i]])},hscale=1.7,vscale=1.07)
ma_img2<<-ma_img
tkpack(ma_img2)
}else{
ma_img2<<-tkrreplot(ma_img,function(...){plot(sample.clust_Ag2[[tag2_i]])},hscale=1.7,vscale=1.07)
}
p_enter_clust<-tcl(treeview,"insert",p_enter,"end",values=as.tclObj("...Clustering"))
setTkProgressBar(pb_ma,0.95,title="Classification...",label="")
er_x<-try(use_DE_Ag2<-as.matrix(DE_Ag2),silent=TRUE)
if(length(grep("Error",er_x))!=0)
{
rownames(DE_Ag2)<-as.character(DE_Ag2)
use_DE_Ag2<-as.matrix(DE_Ag2)
}
rnames<-rownames(use_DE_Ag2)
clas_Ag2[[tag2_i]]<<-as.matrix(use.datAgTwo2.m[rnames,])
if(is.null(ma_img)==TRUE){
try(tkpack.forget(tableData,scrX,scrY),silent=TRUE)
try(tkwm.withdraw(w_legend),silent=TRUE)
ma_img<<-tkrplot(getToolkitWidget(ma_frame2),function(...){
heatmap(clas_Ag2[[tag2_i]],Rowv=NA,Colv=NA,cexCol=0.8,cexRow=0.8,col=heatcol)
},hscale=1.7,vscale=1.07)
ma_img2<<-ma_img
tkpack(ma_img2)
}else{
ma_img2<<-tkrreplot(ma_img,function(...){
heatmap(clas_Ag2[[tag2_i]],Rowv=NA,Colv=NA,cexCol=0.8,cexRow=0.8,col=heatcol)
},hscale=1.7,vscale=1.07)
}
p_enter_class<-tcl(treeview,"insert",p_enter,"end",values=as.tclObj("...Classification"))
setTkProgressBar(pb_ma,1,title="Completed...",label="")
close(pb_ma)
}
}
}
display()
}
pb_ma<-tkProgressBar(title="Loading packages...",label="",min=0,max=1,initial=0,width=500)
setTkProgressBar(pb_ma,0.2,title=NULL,label="")
if(!requireNamespace("gWidgets2tcltk",quietly=TRUE)){install.packages("gWidgets2tcltk");library(gWidgets2tcltk)} else {library(gWidgets2tcltk)}
setTkProgressBar(pb_ma,0.3,title=NULL,label="")
if(!requireNamespace("tkrplot",quietly=TRUE)){install.packages("tkrplot");library(tkrplot)} else {library(tkrplot)}
setTkProgressBar(pb_ma,0.4,title=NULL,label="")
if(!requireNamespace("BiocManager",quietly=TRUE)){install.packages("BiocManager");library(BiocManager)} else {library(BiocManager)}
setTkProgressBar(pb_ma,0.6,title=NULL,label="")
if(!requireNamespace("genefilter",quietly=TRUE)){BiocManager::install("genefilter",ask=FALSE,update=FALSE);library(genefilter)} else {library(genefilter)}
setTkProgressBar(pb_ma,0.7,title=NULL,label="")
if(!requireNamespace("limma",quietly=TRUE)){BiocManager::install("limma",ask=FALSE,update=FALSE);library(limma)} else {library(limma)}
setTkProgressBar(pb_ma,0.8,title=NULL,label="")
if(!requireNamespace("stats",quietly=TRUE)){install.packages("stats",ask=FALSE,update=FALSE);library(stats)} else {library(stats)}
setTkProgressBar(pb_ma,0.9,title=NULL,label="")
if(!requireNamespace("tcltk",quietly=TRUE)){install.packages("tcltk",ask=FALSE,update=FALSE);library(tcltk)} else {library(tcltk)}
setTkProgressBar(pb_ma,1,title="Done...",label="")
close(pb_ma)
agtwo()
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