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inst/extdata/graph_gsta_gobp2.R
In maGUI: A Graphical User Interface for Microarray Data Analysis and Annotation
graph_gsta_gobp<-function(h,...){
graph_gsta_goBP_params<-function(h,h2,h3,h4,h5,h6,h7,...){
ts_name=h;ts_val=h2;gobp<-h3;p_v_1<-h4;p_v_2<-h5;children=h6;r_choice=h7;
pb_ma<-tkProgressBar(title="Graph GSTA GO Biological Process...",label="",min=0,max=1,initial=0.1,width=500)
setTkProgressBar(pb_ma,0.1,title=NULL,label="")
p1<-rownames(gobp)[gobp$'p-value'>=p_v_1]
p2<-rownames(gobp)[gobp$'p-value'<=p_v_2]
p<-p2[match(p1,p2)]
GO.vec<-p[!is.na(p)==TRUE]
g<-GOGraph(GO.vec,GOBPPARENTS)
setTkProgressBar(pb_ma,0.5,title=NULL,label="")
g<-removeNode("all",g)
nodes<-buildNodeList(g)
focusnode<-sapply(nodes,name) %in% GO.vec
names(focusnode)<-names(nodes)
nodefill<-ifelse(focusnode,"yellow","white")
nAttrs<-list()
nAttrs$fillcolor<-nodefill
graph_gsta_goBP<-plot(g,nodeAttrs=nAttrs)
setTkProgressBar(pb_ma,0.8,title=NULL,label="")
terms<-getGOTerm(nodes(g))
legend<-data.frame(terms)
g_colrs<-data.frame(nodefill)
legend_gsta_goBP<-data.frame(g_colrs,legend)
colnames(legend_gsta_goBP)<-c("Node_Color","BP")
setTkProgressBar(pb_ma,0.9,title=NULL,label="")
ta_legend_gsta_gobp<-tclArray()
for(i in 0:dim(legend_gsta_goBP)[1]){ for(j in 0:dim(legend_gsta_goBP)[2]){
if(i==0){ ta_legend_gsta_gobp[[i,j]]<-colnames(legend_gsta_goBP)[j] } else {
if(j==0){ ta_legend_gsta_gobp[[i,j]]<-rownames(legend_gsta_goBP)[i] } else {
tem<-legend_gsta_goBP[i,j]
ta_legend_gsta_gobp[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
} }
} }
setTkProgressBar(pb_ma,1,title="Completed...",label="")
close(pb_ma)
if(ts_name=="Affymetrix"){
graph_gsta_goBP_Affy[[ts_val]]<<-g
nodefill_gsta_goBP_Affy[[ts_val]]<<-nodefill
legend_gsta_goBP_Affy[[ts_val]]<<-legend_gsta_goBP
ta_affy_legend_gsta_gobp[[ts_val]]<<-ta_legend_gsta_gobp
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(graph_gsta_goBP_Affy[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
ma_img2<<-ma_img
tkpack(ma_img2)
}else{
ma_img2<<-tkrreplot(ma_img,function(...){plot(graph_gsta_goBP_Affy[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
}
for(i in 1:length(children)){
x<-as.character(tcl(treeview,"item",children[i],"-values"))
if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...GSTA_GOBP_Graph"))
}
legend_tab(ta_affy_legend_gsta_gobp[[ts_val]],nrow(legend_gsta_goBP_Affy[[ts_val]]),ncol(legend_gsta_goBP_Affy[[ts_val]]),"GSTA_GOBP_Graph_Legend")
}
if(ts_name=="Agilent-OneColor"){
graph_gsta_goBP_Ag1[[ts_val]]<<-g
nodefill_gsta_goBP_Ag1[[ts_val]]<<-nodefill
legend_gsta_goBP_Ag1[[ts_val]]<<-legend_gsta_goBP
ta_ag1_legend_gsta_gobp[[ts_val]]<<-ta_legend_gsta_gobp
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(graph_gsta_goBP_Ag1[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
ma_img2<<-ma_img
tkpack(ma_img2)
}else{
ma_img2<<-tkrreplot(ma_img,function(...){plot(graph_gsta_goBP_Ag1[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
}
for(i in 1:length(children)){
x<-as.character(tcl(treeview,"item",children[i],"-values"))
if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...GSTA_GOBP_Graph"))
}
legend_tab(ta_ag1_legend_gsta_gobp[[ts_val]],nrow(legend_gsta_goBP_Ag1[[ts_val]]),ncol(legend_gsta_goBP_Ag1[[ts_val]]),"GSTA_GOBP_Graph_Legend")
}
if(ts_name=="Agilent-TwoColor"){
graph_gsta_goBP_Ag2[[ts_val]]<<-g
nodefill_gsta_goBP_Ag2[[ts_val]]<<-nodefill
legend_gsta_goBP_Ag2[[ts_val]]<<-legend_gsta_goBP
ta_ag2_legend_gsta_gobp[[ts_val]]<<-ta_legend_gsta_gobp
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(graph_gsta_goBP_Ag2[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
ma_img2<<-ma_img
tkpack(ma_img2)
}else{
ma_img2<<-tkrreplot(ma_img,function(...){plot(graph_gsta_goBP_Ag2[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
}
for(i in 1:length(children)){
x<-as.character(tcl(treeview,"item",children[i],"-values"))
if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...GSTA_GOBP_Graph"))
}
legend_tab(ta_ag2_legend_gsta_gobp[[ts_val]],nrow(legend_gsta_goBP_Ag2[[ts_val]]),ncol(legend_gsta_goBP_Ag2[[ts_val]]),"GSTA_GOBP_Graph_Legend")
}
if(ts_name=="Illumina-Beadarray"){
graph_gsta_goBP_Il_B[[ts_val]]<<-g
nodefill_gsta_goBP_Il_B[[ts_val]]<<-nodefill
legend_gsta_goBP_Il_B[[ts_val]]<<-legend_gsta_goBP
ta_ilb_legend_gsta_gobp[[ts_val]]<<-ta_legend_gsta_gobp
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(graph_gsta_goBP_Il_B[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
ma_img2<<-ma_img
tkpack(ma_img2)
}else{
ma_img2<<-tkrreplot(ma_img,function(...){plot(graph_gsta_goBP_Il_B[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
}
for(i in 1:length(children)){
x<-as.character(tcl(treeview,"item",children[i],"-values"))
if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...GSTA_GOBP_Graph"))
}
legend_tab(ta_ilb_legend_gsta_gobp[[ts_val]],nrow(legend_gsta_goBP_Il_B[[ts_val]]),ncol(legend_gsta_goBP_Il_B[[ts_val]]),"GSTA_GOBP_Graph_Legend")
}
if(ts_name=="Illumina-Lumi"){
graph_gsta_goBP_Il_L[[ts_val]]<<-g
nodefill_gsta_goBP_Il_L[[ts_val]]<<-nodefill
legend_gsta_goBP_Il_L[[ts_val]]<<-legend_gsta_goBP
ta_ill_legend_gsta_gobp[[ts_val]]<<-ta_legend_gsta_gobp
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(graph_gsta_goBP_Il_L[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
ma_img2<<-ma_img
tkpack(ma_img2)
}else{
ma_img2<<-tkrreplot(ma_img,function(...){plot(graph_gsta_goBP_Il_L[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
}
for(i in 1:length(children)){
x<-as.character(tcl(treeview,"item",children[i],"-values"))
if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...GSTA_GOBP_Graph"))
}
legend_tab(ta_ill_legend_gsta_gobp[[ts_val]],nrow(legend_gsta_goBP_Il_L[[ts_val]]),ncol(legend_gsta_goBP_Il_L[[ts_val]]),"GSTA_GOBP_Graph_Legend")
}
if(ts_name=="Nimblegen"){
graph_gsta_goBP_N[[ts_val]]<<-g
nodefill_gsta_goBP_N[[ts_val]]<<-nodefill
legend_gsta_goBP_N[[ts_val]]<<-legend_gsta_goBP
ta_nbl_legend_gsta_gobp[[ts_val]]<<-ta_legend_gsta_gobp
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(graph_gsta_goBP_N[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
ma_img2<<-ma_img
tkpack(ma_img2)
}else{
ma_img2<<-tkrreplot(ma_img,function(...){plot(graph_gsta_goBP_N[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
}
for(i in 1:length(children)){
x<-as.character(tcl(treeview,"item",children[i],"-values"))
if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...GSTA_GOBP_Graph"))
}
legend_tab(ta_nbl_legend_gsta_gobp[[ts_val]],nrow(legend_gsta_goBP_N[[ts_val]]),ncol(legend_gsta_goBP_N[[ts_val]]),"GSTA_GOBP_Graph_Legend")
}
if(ts_name=="Series-Matrix"){
graph_gsta_goBP_S[[ts_val]]<<-g
nodefill_gsta_goBP_S[[ts_val]]<<-nodefill
legend_gsta_goBP_S[[ts_val]]<<-legend_gsta_goBP
ta_smt_legend_gsta_gobp[[ts_val]]<<-ta_legend_gsta_gobp
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(graph_gsta_goBP_S[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
ma_img2<<-ma_img
tkpack(ma_img2)
}else{
ma_img2<<-tkrreplot(ma_img,function(...){plot(graph_gsta_goBP_S[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
}
for(i in 1:length(children)){
x<-as.character(tcl(treeview,"item",children[i],"-values"))
if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...GSTA_GOBP_Graph"))
}
legend_tab(ta_smt_legend_gsta_gobp[[ts_val]],nrow(legend_gsta_goBP_S[[ts_val]]),ncol(legend_gsta_goBP_S[[ts_val]]),"GSTA_GOBP_Graph_Legend")
}
if(ts_name=="Online-Data"){
graph_gsta_goBP_O[[ts_val]]<<-g
nodefill_gsta_goBP_O[[ts_val]]<<-nodefill
legend_gsta_goBP_O[[ts_val]]<<-legend_gsta_goBP
ta_onl_legend_gsta_gobp[[ts_val]]<<-ta_legend_gsta_gobp
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(graph_gsta_goBP_O[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
ma_img2<<-ma_img
tkpack(ma_img2)
}else{
ma_img2<<-tkrreplot(ma_img,function(...){plot(graph_gsta_goBP_O[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
}
for(i in 1:length(children)){
x<-as.character(tcl(treeview,"item",children[i],"-values"))
if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...GSTA_GOBP_Graph"))
}
legend_tab(ta_onl_legend_gsta_gobp[[ts_val]],nrow(legend_gsta_goBP_O[[ts_val]]),ncol(legend_gsta_goBP_O[[ts_val]]),"GSTA_GOBP_Graph_Legend")
}
}
r_choice="._."
children<-as.character(tcl(treeview,"children",""))
w_analz<-tktoplevel()
w_analz_frame<-ttkframe(w_analz,padding=c(3,3,50,20),borderwidth=1,relief="groove")
tkpack(w_analz_frame,expand=TRUE,fill="both",side="left")
var<-tclVar(tree_prnts[1])
sapply(tree_prnts,function(i){
r_but_vals<-ttkradiobutton(w_analz_frame,variable=var,text=i,value=i)
tkpack(r_but_vals,side="top",anchor="w")
})
tkpack(ttklabel(w_analz_frame,text=''))
tkpack(ttklabel(w_analz_frame,text=''))
r_but<-ttkbutton(w_analz_frame,text="Ok")
tkpack(r_but,pady=2)
tkconfigure(r_but,command=function(){
r_choice<-tclvalue(var)
tkwm.withdraw(w_analz)
tree_slc<-strsplit(r_choice[1],"_")
ts_name<-tree_slc[[1]][1]
ts_val<-as.numeric(tree_slc[[1]][2])
w_imp<-tktoplevel()
tkwm.title(w_imp,"Select P-values")
tkwm.resizable(w_imp,0,0)
frame_imp<-ttkframe(w_imp,padding=c(3,3,12,12))
tkpack(ttklabel(frame_imp,text='Lower limit'),side="left",padx=30)
tkpack(ttklabel(frame_imp,text='Upper limit'),side="left",padx=30)
tkpack(frame_imp,expand=TRUE,fill="both",side="top")
frame2_imp<-ttkframe(w_imp,padding=c(3,3,12,12))
p_list<-c(1,0.5,0.1,0.05,0.01,0.001,0.0001,0.00001,0.0000000001,0)
p_value1<-tclVar(p_list[5])
p_comb1<-ttkcombobox(frame2_imp,values=p_list,textvariable=p_value1,state="normal",justify="left",width=10)
tkpack(p_comb1,side="left",padx=25)
p_value2<-tclVar(p_list[4])
p_comb2<-ttkcombobox(frame2_imp,values=p_list,textvariable=p_value2,state="normal",justify="left",width=10)
tkpack(p_comb2,side="left",padx=12)
tkpack(frame2_imp,expand=TRUE,fill="both",side="top")
frame3_imp<-ttkframe(w_imp,padding=c(3,3,12,12))
r_but<-ttkbutton(frame3_imp,text="Ok")
tkpack(r_but,side="right",padx=12)
tkpack(frame3_imp,expand=TRUE,fill="both",side="top")
tkconfigure(r_but,command=function(){
tkwm.withdraw(w_imp)
p_v_1<-as.numeric(tclvalue(p_value1))
p_v_2<-as.numeric(tclvalue(p_value2))
if(ts_name=="Affymetrix"){
graph_gsta_goBP_params(ts_name,ts_val,GOtable.outBP_Affy[[ts_val]],p_v_1,p_v_2,children,r_choice)
}
if(ts_name=="Agilent-OneColor"){
graph_gsta_goBP_params(ts_name,ts_val,GOtable.outBP_Ag1[[ts_val]],p_v_1,p_v_2,children,r_choice)
}
if(ts_name=="Agilent-TwoColor"){
graph_gsta_goBP_params(ts_name,ts_val,GOtable.outBP_Ag2[[ts_val]],p_v_1,p_v_2,children,r_choice)
}
if(ts_name=="Illumina-Beadarray"){
graph_gsta_goBP_params(ts_name,ts_val,GOtable.outBP_Il_B[[ts_val]],p_v_1,p_v_2,children,r_choice)
}
if(ts_name=="Illumina-Lumi"){
graph_gsta_goBP_params(ts_name,ts_val,GOtable.outBP_Il_L[[ts_val]],p_v_1,p_v_2,children,r_choice)
}
if(ts_name=="Nimblegen"){
graph_gsta_goBP_params(ts_name,ts_val,GOtable.outBP_N[[ts_val]],p_v_1,p_v_2,children,r_choice)
}
if(ts_name=="Series-Matrix"){
graph_gsta_goBP_params(ts_name,ts_val,GOtable.outBP_S[[ts_val]],p_v_1,p_v_2,children,r_choice)
}
if(ts_name=="Online-Data"){
graph_gsta_goBP_params(ts_name,ts_val,GOtable.outBP_O[[ts_val]],p_v_1,p_v_2,children,r_choice)
}
})
})
}
pb_ma<-tkProgressBar(title="Loading packages...",label="",min=0,max=1,initial=0,width=500)
setTkProgressBar(pb_ma,0.1,title=NULL,label="")
if(!requireNamespace("gWidgets2tcltk",quietly=TRUE)){install.packages("gWidgets2tcltk");library(gWidgets2tcltk)} else {library(gWidgets2tcltk)}
setTkProgressBar(pb_ma,0.2,title=NULL,label="")
if(!requireNamespace("tkrplot",quietly=TRUE)){install.packages("tkrplot");library(tkrplot)} else {library(tkrplot)}
setTkProgressBar(pb_ma,0.3,title=NULL,label="")
if(!requireNamespace("BiocManager",quietly=TRUE)){install.packages("BiocManager");library(BiocManager)} else {library(BiocManager)}
setTkProgressBar(pb_ma,0.4,title=NULL,label="")
if(!requireNamespace("annotate",quietly=TRUE)){BiocManager::install("annotate",ask=FALSE,update=FALSE);library(annotate)} else {library(annotate)}
setTkProgressBar(pb_ma,0.5,title=NULL,label="")
if(!requireNamespace("GO.db",quietly=TRUE)){BiocManager::install("GO.db",ask=FALSE,update=FALSE);library(GO.db)} else {library(GO.db)}
setTkProgressBar(pb_ma,0.6,title=NULL,label="")
if(!requireNamespace("GOstats",quietly=TRUE)){BiocManager::install("GOstats",ask=FALSE,update=FALSE);library(GOstats)} else {library(GOstats)}
setTkProgressBar(pb_ma,0.7,title=NULL,label="")
if(!requireNamespace("graph",quietly=TRUE)){BiocManager::install("graph",ask=FALSE,update=FALSE);library(graph)} else {library(graph)}
setTkProgressBar(pb_ma,0.8,title=NULL,label="")
if(!requireNamespace("Rgraphviz",quietly=TRUE)){install.packages("Rgraphviz",ask=FALSE,update=FALSE);library(Rgraphviz)} else {library(Rgraphviz)}
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)
graph_gsta_gobp()
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graph_gsta_gobp<-function(h,...){
graph_gsta_goBP_params<-function(h,h2,h3,h4,h5,h6,h7,...){
ts_name=h;ts_val=h2;gobp<-h3;p_v_1<-h4;p_v_2<-h5;children=h6;r_choice=h7;
pb_ma<-tkProgressBar(title="Graph GSTA GO Biological Process...",label="",min=0,max=1,initial=0.1,width=500)
setTkProgressBar(pb_ma,0.1,title=NULL,label="")
p1<-rownames(gobp)[gobp$'p-value'>=p_v_1]
p2<-rownames(gobp)[gobp$'p-value'<=p_v_2]
p<-p2[match(p1,p2)]
GO.vec<-p[!is.na(p)==TRUE]
g<-GOGraph(GO.vec,GOBPPARENTS)
setTkProgressBar(pb_ma,0.5,title=NULL,label="")
g<-removeNode("all",g)
nodes<-buildNodeList(g)
focusnode<-sapply(nodes,name) %in% GO.vec
names(focusnode)<-names(nodes)
nodefill<-ifelse(focusnode,"yellow","white")
nAttrs<-list()
nAttrs$fillcolor<-nodefill
graph_gsta_goBP<-plot(g,nodeAttrs=nAttrs)
setTkProgressBar(pb_ma,0.8,title=NULL,label="")
terms<-getGOTerm(nodes(g))
legend<-data.frame(terms)
g_colrs<-data.frame(nodefill)
legend_gsta_goBP<-data.frame(g_colrs,legend)
colnames(legend_gsta_goBP)<-c("Node_Color","BP")
setTkProgressBar(pb_ma,0.9,title=NULL,label="")
ta_legend_gsta_gobp<-tclArray()
for(i in 0:dim(legend_gsta_goBP)[1]){ for(j in 0:dim(legend_gsta_goBP)[2]){
if(i==0){ ta_legend_gsta_gobp[[i,j]]<-colnames(legend_gsta_goBP)[j] } else {
if(j==0){ ta_legend_gsta_gobp[[i,j]]<-rownames(legend_gsta_goBP)[i] } else {
tem<-legend_gsta_goBP[i,j]
ta_legend_gsta_gobp[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
} }
} }
setTkProgressBar(pb_ma,1,title="Completed...",label="")
close(pb_ma)
if(ts_name=="Affymetrix"){
graph_gsta_goBP_Affy[[ts_val]]<<-g
nodefill_gsta_goBP_Affy[[ts_val]]<<-nodefill
legend_gsta_goBP_Affy[[ts_val]]<<-legend_gsta_goBP
ta_affy_legend_gsta_gobp[[ts_val]]<<-ta_legend_gsta_gobp
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(graph_gsta_goBP_Affy[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
ma_img2<<-ma_img
tkpack(ma_img2)
}else{
ma_img2<<-tkrreplot(ma_img,function(...){plot(graph_gsta_goBP_Affy[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
}
for(i in 1:length(children)){
x<-as.character(tcl(treeview,"item",children[i],"-values"))
if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...GSTA_GOBP_Graph"))
}
legend_tab(ta_affy_legend_gsta_gobp[[ts_val]],nrow(legend_gsta_goBP_Affy[[ts_val]]),ncol(legend_gsta_goBP_Affy[[ts_val]]),"GSTA_GOBP_Graph_Legend")
}
if(ts_name=="Agilent-OneColor"){
graph_gsta_goBP_Ag1[[ts_val]]<<-g
nodefill_gsta_goBP_Ag1[[ts_val]]<<-nodefill
legend_gsta_goBP_Ag1[[ts_val]]<<-legend_gsta_goBP
ta_ag1_legend_gsta_gobp[[ts_val]]<<-ta_legend_gsta_gobp
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(graph_gsta_goBP_Ag1[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
ma_img2<<-ma_img
tkpack(ma_img2)
}else{
ma_img2<<-tkrreplot(ma_img,function(...){plot(graph_gsta_goBP_Ag1[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
}
for(i in 1:length(children)){
x<-as.character(tcl(treeview,"item",children[i],"-values"))
if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...GSTA_GOBP_Graph"))
}
legend_tab(ta_ag1_legend_gsta_gobp[[ts_val]],nrow(legend_gsta_goBP_Ag1[[ts_val]]),ncol(legend_gsta_goBP_Ag1[[ts_val]]),"GSTA_GOBP_Graph_Legend")
}
if(ts_name=="Agilent-TwoColor"){
graph_gsta_goBP_Ag2[[ts_val]]<<-g
nodefill_gsta_goBP_Ag2[[ts_val]]<<-nodefill
legend_gsta_goBP_Ag2[[ts_val]]<<-legend_gsta_goBP
ta_ag2_legend_gsta_gobp[[ts_val]]<<-ta_legend_gsta_gobp
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(graph_gsta_goBP_Ag2[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
ma_img2<<-ma_img
tkpack(ma_img2)
}else{
ma_img2<<-tkrreplot(ma_img,function(...){plot(graph_gsta_goBP_Ag2[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
}
for(i in 1:length(children)){
x<-as.character(tcl(treeview,"item",children[i],"-values"))
if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...GSTA_GOBP_Graph"))
}
legend_tab(ta_ag2_legend_gsta_gobp[[ts_val]],nrow(legend_gsta_goBP_Ag2[[ts_val]]),ncol(legend_gsta_goBP_Ag2[[ts_val]]),"GSTA_GOBP_Graph_Legend")
}
if(ts_name=="Illumina-Beadarray"){
graph_gsta_goBP_Il_B[[ts_val]]<<-g
nodefill_gsta_goBP_Il_B[[ts_val]]<<-nodefill
legend_gsta_goBP_Il_B[[ts_val]]<<-legend_gsta_goBP
ta_ilb_legend_gsta_gobp[[ts_val]]<<-ta_legend_gsta_gobp
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(graph_gsta_goBP_Il_B[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
ma_img2<<-ma_img
tkpack(ma_img2)
}else{
ma_img2<<-tkrreplot(ma_img,function(...){plot(graph_gsta_goBP_Il_B[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
}
for(i in 1:length(children)){
x<-as.character(tcl(treeview,"item",children[i],"-values"))
if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...GSTA_GOBP_Graph"))
}
legend_tab(ta_ilb_legend_gsta_gobp[[ts_val]],nrow(legend_gsta_goBP_Il_B[[ts_val]]),ncol(legend_gsta_goBP_Il_B[[ts_val]]),"GSTA_GOBP_Graph_Legend")
}
if(ts_name=="Illumina-Lumi"){
graph_gsta_goBP_Il_L[[ts_val]]<<-g
nodefill_gsta_goBP_Il_L[[ts_val]]<<-nodefill
legend_gsta_goBP_Il_L[[ts_val]]<<-legend_gsta_goBP
ta_ill_legend_gsta_gobp[[ts_val]]<<-ta_legend_gsta_gobp
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(graph_gsta_goBP_Il_L[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
ma_img2<<-ma_img
tkpack(ma_img2)
}else{
ma_img2<<-tkrreplot(ma_img,function(...){plot(graph_gsta_goBP_Il_L[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
}
for(i in 1:length(children)){
x<-as.character(tcl(treeview,"item",children[i],"-values"))
if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...GSTA_GOBP_Graph"))
}
legend_tab(ta_ill_legend_gsta_gobp[[ts_val]],nrow(legend_gsta_goBP_Il_L[[ts_val]]),ncol(legend_gsta_goBP_Il_L[[ts_val]]),"GSTA_GOBP_Graph_Legend")
}
if(ts_name=="Nimblegen"){
graph_gsta_goBP_N[[ts_val]]<<-g
nodefill_gsta_goBP_N[[ts_val]]<<-nodefill
legend_gsta_goBP_N[[ts_val]]<<-legend_gsta_goBP
ta_nbl_legend_gsta_gobp[[ts_val]]<<-ta_legend_gsta_gobp
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(graph_gsta_goBP_N[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
ma_img2<<-ma_img
tkpack(ma_img2)
}else{
ma_img2<<-tkrreplot(ma_img,function(...){plot(graph_gsta_goBP_N[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
}
for(i in 1:length(children)){
x<-as.character(tcl(treeview,"item",children[i],"-values"))
if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...GSTA_GOBP_Graph"))
}
legend_tab(ta_nbl_legend_gsta_gobp[[ts_val]],nrow(legend_gsta_goBP_N[[ts_val]]),ncol(legend_gsta_goBP_N[[ts_val]]),"GSTA_GOBP_Graph_Legend")
}
if(ts_name=="Series-Matrix"){
graph_gsta_goBP_S[[ts_val]]<<-g
nodefill_gsta_goBP_S[[ts_val]]<<-nodefill
legend_gsta_goBP_S[[ts_val]]<<-legend_gsta_goBP
ta_smt_legend_gsta_gobp[[ts_val]]<<-ta_legend_gsta_gobp
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(graph_gsta_goBP_S[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
ma_img2<<-ma_img
tkpack(ma_img2)
}else{
ma_img2<<-tkrreplot(ma_img,function(...){plot(graph_gsta_goBP_S[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
}
for(i in 1:length(children)){
x<-as.character(tcl(treeview,"item",children[i],"-values"))
if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...GSTA_GOBP_Graph"))
}
legend_tab(ta_smt_legend_gsta_gobp[[ts_val]],nrow(legend_gsta_goBP_S[[ts_val]]),ncol(legend_gsta_goBP_S[[ts_val]]),"GSTA_GOBP_Graph_Legend")
}
if(ts_name=="Online-Data"){
graph_gsta_goBP_O[[ts_val]]<<-g
nodefill_gsta_goBP_O[[ts_val]]<<-nodefill
legend_gsta_goBP_O[[ts_val]]<<-legend_gsta_goBP
ta_onl_legend_gsta_gobp[[ts_val]]<<-ta_legend_gsta_gobp
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(graph_gsta_goBP_O[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
ma_img2<<-ma_img
tkpack(ma_img2)
}else{
ma_img2<<-tkrreplot(ma_img,function(...){plot(graph_gsta_goBP_O[[ts_val]],nodeAttrs=nAttrs)},hscale=1.7,vscale=1.07)
}
for(i in 1:length(children)){
x<-as.character(tcl(treeview,"item",children[i],"-values"))
if(x==r_choice[1])p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...GSTA_GOBP_Graph"))
}
legend_tab(ta_onl_legend_gsta_gobp[[ts_val]],nrow(legend_gsta_goBP_O[[ts_val]]),ncol(legend_gsta_goBP_O[[ts_val]]),"GSTA_GOBP_Graph_Legend")
}
}
r_choice="._."
children<-as.character(tcl(treeview,"children",""))
w_analz<-tktoplevel()
w_analz_frame<-ttkframe(w_analz,padding=c(3,3,50,20),borderwidth=1,relief="groove")
tkpack(w_analz_frame,expand=TRUE,fill="both",side="left")
var<-tclVar(tree_prnts[1])
sapply(tree_prnts,function(i){
r_but_vals<-ttkradiobutton(w_analz_frame,variable=var,text=i,value=i)
tkpack(r_but_vals,side="top",anchor="w")
})
tkpack(ttklabel(w_analz_frame,text=''))
tkpack(ttklabel(w_analz_frame,text=''))
r_but<-ttkbutton(w_analz_frame,text="Ok")
tkpack(r_but,pady=2)
tkconfigure(r_but,command=function(){
r_choice<-tclvalue(var)
tkwm.withdraw(w_analz)
tree_slc<-strsplit(r_choice[1],"_")
ts_name<-tree_slc[[1]][1]
ts_val<-as.numeric(tree_slc[[1]][2])
w_imp<-tktoplevel()
tkwm.title(w_imp,"Select P-values")
tkwm.resizable(w_imp,0,0)
frame_imp<-ttkframe(w_imp,padding=c(3,3,12,12))
tkpack(ttklabel(frame_imp,text='Lower limit'),side="left",padx=30)
tkpack(ttklabel(frame_imp,text='Upper limit'),side="left",padx=30)
tkpack(frame_imp,expand=TRUE,fill="both",side="top")
frame2_imp<-ttkframe(w_imp,padding=c(3,3,12,12))
p_list<-c(1,0.5,0.1,0.05,0.01,0.001,0.0001,0.00001,0.0000000001,0)
p_value1<-tclVar(p_list[5])
p_comb1<-ttkcombobox(frame2_imp,values=p_list,textvariable=p_value1,state="normal",justify="left",width=10)
tkpack(p_comb1,side="left",padx=25)
p_value2<-tclVar(p_list[4])
p_comb2<-ttkcombobox(frame2_imp,values=p_list,textvariable=p_value2,state="normal",justify="left",width=10)
tkpack(p_comb2,side="left",padx=12)
tkpack(frame2_imp,expand=TRUE,fill="both",side="top")
frame3_imp<-ttkframe(w_imp,padding=c(3,3,12,12))
r_but<-ttkbutton(frame3_imp,text="Ok")
tkpack(r_but,side="right",padx=12)
tkpack(frame3_imp,expand=TRUE,fill="both",side="top")
tkconfigure(r_but,command=function(){
tkwm.withdraw(w_imp)
p_v_1<-as.numeric(tclvalue(p_value1))
p_v_2<-as.numeric(tclvalue(p_value2))
if(ts_name=="Affymetrix"){
graph_gsta_goBP_params(ts_name,ts_val,GOtable.outBP_Affy[[ts_val]],p_v_1,p_v_2,children,r_choice)
}
if(ts_name=="Agilent-OneColor"){
graph_gsta_goBP_params(ts_name,ts_val,GOtable.outBP_Ag1[[ts_val]],p_v_1,p_v_2,children,r_choice)
}
if(ts_name=="Agilent-TwoColor"){
graph_gsta_goBP_params(ts_name,ts_val,GOtable.outBP_Ag2[[ts_val]],p_v_1,p_v_2,children,r_choice)
}
if(ts_name=="Illumina-Beadarray"){
graph_gsta_goBP_params(ts_name,ts_val,GOtable.outBP_Il_B[[ts_val]],p_v_1,p_v_2,children,r_choice)
}
if(ts_name=="Illumina-Lumi"){
graph_gsta_goBP_params(ts_name,ts_val,GOtable.outBP_Il_L[[ts_val]],p_v_1,p_v_2,children,r_choice)
}
if(ts_name=="Nimblegen"){
graph_gsta_goBP_params(ts_name,ts_val,GOtable.outBP_N[[ts_val]],p_v_1,p_v_2,children,r_choice)
}
if(ts_name=="Series-Matrix"){
graph_gsta_goBP_params(ts_name,ts_val,GOtable.outBP_S[[ts_val]],p_v_1,p_v_2,children,r_choice)
}
if(ts_name=="Online-Data"){
graph_gsta_goBP_params(ts_name,ts_val,GOtable.outBP_O[[ts_val]],p_v_1,p_v_2,children,r_choice)
}
})
})
}
pb_ma<-tkProgressBar(title="Loading packages...",label="",min=0,max=1,initial=0,width=500)
setTkProgressBar(pb_ma,0.1,title=NULL,label="")
if(!requireNamespace("gWidgets2tcltk",quietly=TRUE)){install.packages("gWidgets2tcltk");library(gWidgets2tcltk)} else {library(gWidgets2tcltk)}
setTkProgressBar(pb_ma,0.2,title=NULL,label="")
if(!requireNamespace("tkrplot",quietly=TRUE)){install.packages("tkrplot");library(tkrplot)} else {library(tkrplot)}
setTkProgressBar(pb_ma,0.3,title=NULL,label="")
if(!requireNamespace("BiocManager",quietly=TRUE)){install.packages("BiocManager");library(BiocManager)} else {library(BiocManager)}
setTkProgressBar(pb_ma,0.4,title=NULL,label="")
if(!requireNamespace("annotate",quietly=TRUE)){BiocManager::install("annotate",ask=FALSE,update=FALSE);library(annotate)} else {library(annotate)}
setTkProgressBar(pb_ma,0.5,title=NULL,label="")
if(!requireNamespace("GO.db",quietly=TRUE)){BiocManager::install("GO.db",ask=FALSE,update=FALSE);library(GO.db)} else {library(GO.db)}
setTkProgressBar(pb_ma,0.6,title=NULL,label="")
if(!requireNamespace("GOstats",quietly=TRUE)){BiocManager::install("GOstats",ask=FALSE,update=FALSE);library(GOstats)} else {library(GOstats)}
setTkProgressBar(pb_ma,0.7,title=NULL,label="")
if(!requireNamespace("graph",quietly=TRUE)){BiocManager::install("graph",ask=FALSE,update=FALSE);library(graph)} else {library(graph)}
setTkProgressBar(pb_ma,0.8,title=NULL,label="")
if(!requireNamespace("Rgraphviz",quietly=TRUE)){install.packages("Rgraphviz",ask=FALSE,update=FALSE);library(Rgraphviz)} else {library(Rgraphviz)}
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)
graph_gsta_gobp()
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