R/nodes.R
In sheng-liu/SeqViz: A graphical interface for multidimensional epigenome data exploration
## node operations
##------------------------------------------------------------------------------
## insert.node
## insert node.name into a tree.view
## can insert one or multiple at a time
## method "append" insert node(s) to bottom of the list,
## else insert into selected node
## node.name [character], tree.view [gtkTreeView]
##' @export insert.node
insert.node=function(node.name,tree.view,method=c("insert","append")){
# set parent.iter
parent.iter=if (method=="append") NULL else
tree.view$getSelection()$getSelected()$iter
cat("\nChild nodes:\n")
# add new row(s), correspond to parent.iter
for (i in 1:length(node.name)) {
# add new row depend at the iter location
iter=tree.view$getModel()$append(parent.iter)$iter
# insert node.name
print(node.name[i])
tree.view$getModel()$setValue(iter=iter,column=0,value=node.name[i])
# select on (last) inserted node
path=tree.view$getModel()$getPath(iter)
tree.view$setCursor(path,focus.column=NULL)
}
# expend row when insert
if(!is.null(parent.iter)){
path.parent=tree.view$getModel()$getPath(parent.iter)
tree.view$expandRow(path.parent,open.all=T)
}
# output a signal
#cat(method," node(s):\n",node.name,"\nto:\n",deparse(substitute(tree.view)),"\n")
# since node.name has printed out in the above loop
cat(method," to ",deparse(substitute(tree.view)),"\n")
return(tree.view)
}
# test script
# insert.node(node.name=c("abc","bcd"),tree.view=appspace[SeqFrame.hierachy.view],method="append")
# insert.node(node.name=c("abc","bcd"),tree.view=appspace[SeqFrame.hierachy.view],method="insert")
#parent$getModel()$iterNext(iter$iter)
##------------------------------------------------------------------------------
##------------------------------------------------------------------------------
## selected.node
## return selected node name, and
## change the active.SeqFrame to selected node
## try this function interactively with the GUI, quite fun
##' @export selected.node
selected.node=function(tree.view,setActive=T){
# get selected.node.name
selection=tree.view$getSelection()
iter=gtkTreeSelectionGetSelected(selection)
model=tree.view$getModel()
selected.node.name=model$get(iter=iter$iter,column=0)[[1]]
cat("selected.node.name is: ",selected.node.name,"\n")
if(setActive==T){
# appspace is viewed as public transaction space for all functions
# change the active.SeqFrame to selected node
SeqFrame.list=appspace[SeqFrame.list]
#active.SeqFrame=SeqFrame.list[[names(SeqFrame.list)==selected.node.name]]
active.SeqFrame=SeqFrame.list[
names(SeqFrame.list)==selected.node.name][[selected.node.name]]
appspace[active.SeqFrame]=active.SeqFrame
cat("appspace[active.SeqFrame] set to: ",selected.node.name,"\n")
}
return(selected.node.name)
}
# may change the table.view also to this selelcted.node
# put it in another function so it is easy to manipulate, more flexibility
# update.table(df=exprs(appspace[active.SeqFrame]),table.view=appspace[SeqFrame.table.view])
# this need to be connected to click on the rows of the view via gSignal connect
##------------------------------------------------------------------------------
##------------------------------------------------------------------------------
## select.parent.node
## output selected.node's parent node
## if no parent, output itself
##' @export select.parent.node
select.parent.node=function(tree.view,itself=F){
# get selected node, same as selected.node() function
selection=tree.view$getSelection()
selected_iter=selection$getSelected()
model=tree.view$getModel()
selected.node.name=model$get(iter=selected_iter$iter,column=0)[[1]]
# get parent.node, this only goes one layer up
parent_iter=model$iterParent(child=selected_iter$iter)
# use a list to store parent and itself
parent.node.list=list()
# whether it has parent
has.parent=parent_iter$retval
if (has.parent){
parent.node.list[[1]]=
model$getValue(iter=parent_iter$iter,column=0)$value
# model$get(iter=parent_iter$iter,column=0)[[1]] # also work
}
# whether to add itself
if(itself==T){
parent.node.list$iteself=selected.node.name
}
return(parent.node.list)
}
# You have to be careful with ifelse(); it will return an object with the same length and attributes as the test clause. We can see how this might be a problem via ifelse(FALSE, NA, 1:10), which returns 1, not 1:10. If coef(result)[[1]] is more complex that the test, then your suggestion will fail. It might be syntactically simpler, but it isn't necessarily the right tool here.
## only select parent node, single node
## if there is, output, if there isn't (root), output nothing
## to make it work first, output itself
## so root will be output twice, both by select.all.Child, and select.parent
## output selected.node's parent node
## if no parent, output itself
# it is always lenthg[1] unless you pass in multiple iter
# model$get(iter=parent_iter$iter,column=0)[[1]]
## code could be simpler using ifelse, however it is very tricky sometimes doeson't work, this time it works
# parent.node.name=ifelse(test=parent_iter$retval,
# yes=model$get(iter=parent_iter$iter,column=0)[[1]],
# no=selected.node.name)
# if (!identical(parent.node.name,selected.node.name))
# parent.node.name.list=list(parent.node.name,selected.node.name) else
# parent.node.name.list=list(selected.node.name) # if selected root node
# this will work two, syntax simpler
# parent.node.name.list=
# if (!identical(parent.node.name,selected.node.name))
# list(parent.node.name,selected.node.name) else
# list(selected.node.name)
## this time the ifelse has problem again
## parent.node.name.list only have the first value when it is yes
# parent.node.name.list=ifelse(
# test=!identical(parent.node.name,selected.node.name),
# yes=list(parent.node.name,selected.node.name),
# no=list(selected.node.name)
# )
## TODO:
## when select parent nodes, output all child nodes if has any
## if no child, only ouput itself
## this should be the selct child
##------------------------------------------------------------------------------
## return all child node of selected node
# detect if it has child node
# if has, output all child node names
# if selected node no child, return NULL
# itself=T, return itself in the list
# gtkTreeModelIterHasChild
# gtkTreeModelIterNChildren(object, iter = NULL)
# this only goes one layer down
##' @export select.all.child.node
select.all.child.node=function(tree.view,itself=T){
# get selected node, same as selected.node() function
model=tree.view$getModel()
selection=tree.view$getSelection()
selected_iter=selection$getSelected()
selected.node.name=model$get(iter=selected_iter$iter,column=0)[[1]]
# use a list to collect child node names
child.node.list=list()
# when selected.node have child
has.child=model$iterHasChild(iter=selected_iter$iter)
if (has.child){
n=model$iterNChildren(selected_iter$iter) # total number of child
for (i in 1:n){
# get Nth child's iter
child_iter=model$iterNthChild(parent=selected_iter$iter,i-1)$iter
child.node.name=model$getValue(iter=child_iter,column=0)$value
# model$get(iter=child_iter,column=0)[[1]] # works too
child.node.list[i]=child.node.name
}
}
## whether to add itself
if(itself==T) child.node.list$itself=selected.node.name
return(child.node.list)
}
# child_iter=model$iterNthChild(parent=selected_iter$iter,3)$iter
# model$get(iter=child_iter,column=0)[[1]] # a list
# model$getValue(iter=child_iter,column=0)$value # a character
##------------------------------------------------------------------------------
## delete.node
## using key press event to delete a gtkTeeView node
## connects gtkTreeStore
## gtkTreeStoreRemove(object, iter)
# view is gtkTreeView
# event is key-press-event
# these list approach doesnt work
# list is character, c("bamFile.list","SeqFrame.list","annotationFile.list")
# list is appspace list appspace[bamFileList],appspace[SeqFrame.list],appspace[annotation.list]
##' @export delete.node
delete.node=function(view,event){
key <- event[["keyval"]]
if (key == GDK_Delete){
print(GDK_Delete)
# get selected iter
selection=view$getSelection()
iter=gtkTreeSelectionGetSelected(selection)
model=view$getModel()
# get selected.node.name from corresponding view that is operating
selected.node.name=model$get(iter=iter$iter,column=0)[[1]]
# remove the corresponding nodes in the appspace
# try subset based on name doesn't work, and gConnect doesnt allow pass in new variable
#appspacelist[selected.node.name]=NULL
# betting bamFile, annotationFile and SeqFrameFile won't have the same name
# makes coding much more simple
# remove the corresponding nodes from SeqFrame.list
if(exists("SeqFrame.list",envir=.AppEnv)){
appspace[SeqFrame.list][selected.node.name]=NULL
}
if(exists("bamFile.list",envir=.AppEnv)){
appspace[bamFile.list][selected.node.name]=NULL
}
if(exists("annotationFile.list",envir=.AppEnv)){
appspace[annotationFile.list][selected.node.name]=NULL
}
cat(selected.node.name,"deleted\n")
# redo function can work somewhere here
# if (undo==T){
# insert.node()
# insert.node=function(node.name=selected.node.name,parent=appspace[SeqFrame.hierachy.view],loc="insert")
# }
# remove row
gtkTreeStoreRemove(object=model,iter=iter$iter)
}
}
# > x
# [1] "Demo.csv (H3K9me3-H3K27me3-)"
# # none of these works
# rm(get(x,envir=.AppEnv),envir=.AppEnv)
# get(x,envir=.AppEnv)
# rm(x,envir=.AppEnv)
# rm(basename(x),envir=.AppEnv)
# rm(as.symbol(x),envir=.AppEnv)
#
# # This does the work
# rm(list=x,envir=.AppEnv)
# be careful with ifelse
# > parent.iter1=ifelse(F,NULL,view$getSelection()$getSelected()$iter)
# Error in rep(no, length.out = length(ans)) :
# attempt to replicate an object of type 'externalptr'
# > x=ifelse(2==3,2,3)
# > x
# [1] 3
##------------------------------------------------------------------------------
select.ajacent.node=function(tree.view,up=T){
# two collector
parent.node.name=character(0)
child.node.name=character(0)
# get selected node
# same as selected.node() function
selection=tree.view$getSelection()
selected_iter=selection$getSelected()
model=tree.view$getModel()
selected.node.name=model$get(iter=selected_iter$iter,column=0)[[1]]
# get parent.node
parent_iter=model$iterParent(child=selected_iter$iter)
#print(parent_iter)
# when there is parent node parent_iter$retval==T
if (parent_iter$retval==T){
parent.node.name=model$get(iter=parent_iter$iter,column=0)[[1]]
}
# get child.node
child_iter=model$iterChildren(parent=selected_iter$iter)
#print(child_iter)
# when there is child node parent_iter$retval==T
if (child_iter$retval==T){
child.node.name=model$get(iter=child_iter$iter,column=0)[[1]]
}
if (up==T&(length(parent.node.name)>0))
return(parent.node.name)
else if (length(child.node.name)>0)
return (child.node.name)
else print("No ajacent node find")
}
# determine active.SeqFrame with selection by the user
# once the mouse clicked on, the SeqFrame.hierachy.view and active.model has to be reset to the selected one
# return selected node name
##########################
#appspace[active.model]=gtkTreeViewGetModel(selection)
## there is only one tree view, but there is multiple dataset SeqFrame serve as node to insert and for plot
## tree view is only for display and interaction with user
## there is multiple view, each action creates one or more views, which has its own data store model
## when add nodes, is the new view automatically created, or has to set every time an action applies to a view
# I think it has to be set again
## determine the active seqSet
## holds some variable/parameters/container in appspace when started, change the state of the parameters when actions are taken
## activeSeqSet
#active.SeqFrame=appspace()
#appspace[activeSeqFrame]=NULL
## just set the selected one to be active, no need for multiple workflow, people can open multiple windows to do that, each window, one workflow
# try change the model of the view when one clicked on the subnodes
# always change model to the corresponding selected nodes name
#active.SeqFrame=
{
# gtkTreeModel for the combo boxes
#channelsModel=rGtkDataFrame(x=)
# channelsXcombo=
# channelsYcombo=
#
#
# channels <- colnames(active.SeqFrame())
#
#
#
#
#
#
# if(channelsDialog$run()==GtkResponseType["ok"]) print("chanel selected")
# channels$destroy()
}
#
#x=PlotPage.data.view$getSelection()
#gtkTreeSelectionGetSelected(x)
## everywhere need a function to referen the selected name to underneath SeqFrame
# return selected node name
# selection=appspace[SeqFrame.hierachy.view]$getSelection()
# iter=gtkTreeSelectionGetSelected(selection)
# model=gtkTreeViewGetModel(appspace[SeqFrame.hierachy.view])
# selected.node.name=model$get(iter=iter$iter,column=0)[[1]]
sheng-liu/SeqViz documentation built on May 29, 2019, 9:22 p.m.
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## node operations
##------------------------------------------------------------------------------
## insert.node
## insert node.name into a tree.view
## can insert one or multiple at a time
## method "append" insert node(s) to bottom of the list,
## else insert into selected node
## node.name [character], tree.view [gtkTreeView]
##' @export insert.node
insert.node=function(node.name,tree.view,method=c("insert","append")){
# set parent.iter
parent.iter=if (method=="append") NULL else
tree.view$getSelection()$getSelected()$iter
cat("\nChild nodes:\n")
# add new row(s), correspond to parent.iter
for (i in 1:length(node.name)) {
# add new row depend at the iter location
iter=tree.view$getModel()$append(parent.iter)$iter
# insert node.name
print(node.name[i])
tree.view$getModel()$setValue(iter=iter,column=0,value=node.name[i])
# select on (last) inserted node
path=tree.view$getModel()$getPath(iter)
tree.view$setCursor(path,focus.column=NULL)
}
# expend row when insert
if(!is.null(parent.iter)){
path.parent=tree.view$getModel()$getPath(parent.iter)
tree.view$expandRow(path.parent,open.all=T)
}
# output a signal
#cat(method," node(s):\n",node.name,"\nto:\n",deparse(substitute(tree.view)),"\n")
# since node.name has printed out in the above loop
cat(method," to ",deparse(substitute(tree.view)),"\n")
return(tree.view)
}
# test script
# insert.node(node.name=c("abc","bcd"),tree.view=appspace[SeqFrame.hierachy.view],method="append")
# insert.node(node.name=c("abc","bcd"),tree.view=appspace[SeqFrame.hierachy.view],method="insert")
#parent$getModel()$iterNext(iter$iter)
##------------------------------------------------------------------------------
##------------------------------------------------------------------------------
## selected.node
## return selected node name, and
## change the active.SeqFrame to selected node
## try this function interactively with the GUI, quite fun
##' @export selected.node
selected.node=function(tree.view,setActive=T){
# get selected.node.name
selection=tree.view$getSelection()
iter=gtkTreeSelectionGetSelected(selection)
model=tree.view$getModel()
selected.node.name=model$get(iter=iter$iter,column=0)[[1]]
cat("selected.node.name is: ",selected.node.name,"\n")
if(setActive==T){
# appspace is viewed as public transaction space for all functions
# change the active.SeqFrame to selected node
SeqFrame.list=appspace[SeqFrame.list]
#active.SeqFrame=SeqFrame.list[[names(SeqFrame.list)==selected.node.name]]
active.SeqFrame=SeqFrame.list[
names(SeqFrame.list)==selected.node.name][[selected.node.name]]
appspace[active.SeqFrame]=active.SeqFrame
cat("appspace[active.SeqFrame] set to: ",selected.node.name,"\n")
}
return(selected.node.name)
}
# may change the table.view also to this selelcted.node
# put it in another function so it is easy to manipulate, more flexibility
# update.table(df=exprs(appspace[active.SeqFrame]),table.view=appspace[SeqFrame.table.view])
# this need to be connected to click on the rows of the view via gSignal connect
##------------------------------------------------------------------------------
##------------------------------------------------------------------------------
## select.parent.node
## output selected.node's parent node
## if no parent, output itself
##' @export select.parent.node
select.parent.node=function(tree.view,itself=F){
# get selected node, same as selected.node() function
selection=tree.view$getSelection()
selected_iter=selection$getSelected()
model=tree.view$getModel()
selected.node.name=model$get(iter=selected_iter$iter,column=0)[[1]]
# get parent.node, this only goes one layer up
parent_iter=model$iterParent(child=selected_iter$iter)
# use a list to store parent and itself
parent.node.list=list()
# whether it has parent
has.parent=parent_iter$retval
if (has.parent){
parent.node.list[[1]]=
model$getValue(iter=parent_iter$iter,column=0)$value
# model$get(iter=parent_iter$iter,column=0)[[1]] # also work
}
# whether to add itself
if(itself==T){
parent.node.list$iteself=selected.node.name
}
return(parent.node.list)
}
# You have to be careful with ifelse(); it will return an object with the same length and attributes as the test clause. We can see how this might be a problem via ifelse(FALSE, NA, 1:10), which returns 1, not 1:10. If coef(result)[[1]] is more complex that the test, then your suggestion will fail. It might be syntactically simpler, but it isn't necessarily the right tool here.
## only select parent node, single node
## if there is, output, if there isn't (root), output nothing
## to make it work first, output itself
## so root will be output twice, both by select.all.Child, and select.parent
## output selected.node's parent node
## if no parent, output itself
# it is always lenthg[1] unless you pass in multiple iter
# model$get(iter=parent_iter$iter,column=0)[[1]]
## code could be simpler using ifelse, however it is very tricky sometimes doeson't work, this time it works
# parent.node.name=ifelse(test=parent_iter$retval,
# yes=model$get(iter=parent_iter$iter,column=0)[[1]],
# no=selected.node.name)
# if (!identical(parent.node.name,selected.node.name))
# parent.node.name.list=list(parent.node.name,selected.node.name) else
# parent.node.name.list=list(selected.node.name) # if selected root node
# this will work two, syntax simpler
# parent.node.name.list=
# if (!identical(parent.node.name,selected.node.name))
# list(parent.node.name,selected.node.name) else
# list(selected.node.name)
## this time the ifelse has problem again
## parent.node.name.list only have the first value when it is yes
# parent.node.name.list=ifelse(
# test=!identical(parent.node.name,selected.node.name),
# yes=list(parent.node.name,selected.node.name),
# no=list(selected.node.name)
# )
## TODO:
## when select parent nodes, output all child nodes if has any
## if no child, only ouput itself
## this should be the selct child
##------------------------------------------------------------------------------
## return all child node of selected node
# detect if it has child node
# if has, output all child node names
# if selected node no child, return NULL
# itself=T, return itself in the list
# gtkTreeModelIterHasChild
# gtkTreeModelIterNChildren(object, iter = NULL)
# this only goes one layer down
##' @export select.all.child.node
select.all.child.node=function(tree.view,itself=T){
# get selected node, same as selected.node() function
model=tree.view$getModel()
selection=tree.view$getSelection()
selected_iter=selection$getSelected()
selected.node.name=model$get(iter=selected_iter$iter,column=0)[[1]]
# use a list to collect child node names
child.node.list=list()
# when selected.node have child
has.child=model$iterHasChild(iter=selected_iter$iter)
if (has.child){
n=model$iterNChildren(selected_iter$iter) # total number of child
for (i in 1:n){
# get Nth child's iter
child_iter=model$iterNthChild(parent=selected_iter$iter,i-1)$iter
child.node.name=model$getValue(iter=child_iter,column=0)$value
# model$get(iter=child_iter,column=0)[[1]] # works too
child.node.list[i]=child.node.name
}
}
## whether to add itself
if(itself==T) child.node.list$itself=selected.node.name
return(child.node.list)
}
# child_iter=model$iterNthChild(parent=selected_iter$iter,3)$iter
# model$get(iter=child_iter,column=0)[[1]] # a list
# model$getValue(iter=child_iter,column=0)$value # a character
##------------------------------------------------------------------------------
## delete.node
## using key press event to delete a gtkTeeView node
## connects gtkTreeStore
## gtkTreeStoreRemove(object, iter)
# view is gtkTreeView
# event is key-press-event
# these list approach doesnt work
# list is character, c("bamFile.list","SeqFrame.list","annotationFile.list")
# list is appspace list appspace[bamFileList],appspace[SeqFrame.list],appspace[annotation.list]
##' @export delete.node
delete.node=function(view,event){
key <- event[["keyval"]]
if (key == GDK_Delete){
print(GDK_Delete)
# get selected iter
selection=view$getSelection()
iter=gtkTreeSelectionGetSelected(selection)
model=view$getModel()
# get selected.node.name from corresponding view that is operating
selected.node.name=model$get(iter=iter$iter,column=0)[[1]]
# remove the corresponding nodes in the appspace
# try subset based on name doesn't work, and gConnect doesnt allow pass in new variable
#appspacelist[selected.node.name]=NULL
# betting bamFile, annotationFile and SeqFrameFile won't have the same name
# makes coding much more simple
# remove the corresponding nodes from SeqFrame.list
if(exists("SeqFrame.list",envir=.AppEnv)){
appspace[SeqFrame.list][selected.node.name]=NULL
}
if(exists("bamFile.list",envir=.AppEnv)){
appspace[bamFile.list][selected.node.name]=NULL
}
if(exists("annotationFile.list",envir=.AppEnv)){
appspace[annotationFile.list][selected.node.name]=NULL
}
cat(selected.node.name,"deleted\n")
# redo function can work somewhere here
# if (undo==T){
# insert.node()
# insert.node=function(node.name=selected.node.name,parent=appspace[SeqFrame.hierachy.view],loc="insert")
# }
# remove row
gtkTreeStoreRemove(object=model,iter=iter$iter)
}
}
# > x
# [1] "Demo.csv (H3K9me3-H3K27me3-)"
# # none of these works
# rm(get(x,envir=.AppEnv),envir=.AppEnv)
# get(x,envir=.AppEnv)
# rm(x,envir=.AppEnv)
# rm(basename(x),envir=.AppEnv)
# rm(as.symbol(x),envir=.AppEnv)
#
# # This does the work
# rm(list=x,envir=.AppEnv)
# be careful with ifelse
# > parent.iter1=ifelse(F,NULL,view$getSelection()$getSelected()$iter)
# Error in rep(no, length.out = length(ans)) :
# attempt to replicate an object of type 'externalptr'
# > x=ifelse(2==3,2,3)
# > x
# [1] 3
##------------------------------------------------------------------------------
select.ajacent.node=function(tree.view,up=T){
# two collector
parent.node.name=character(0)
child.node.name=character(0)
# get selected node
# same as selected.node() function
selection=tree.view$getSelection()
selected_iter=selection$getSelected()
model=tree.view$getModel()
selected.node.name=model$get(iter=selected_iter$iter,column=0)[[1]]
# get parent.node
parent_iter=model$iterParent(child=selected_iter$iter)
#print(parent_iter)
# when there is parent node parent_iter$retval==T
if (parent_iter$retval==T){
parent.node.name=model$get(iter=parent_iter$iter,column=0)[[1]]
}
# get child.node
child_iter=model$iterChildren(parent=selected_iter$iter)
#print(child_iter)
# when there is child node parent_iter$retval==T
if (child_iter$retval==T){
child.node.name=model$get(iter=child_iter$iter,column=0)[[1]]
}
if (up==T&(length(parent.node.name)>0))
return(parent.node.name)
else if (length(child.node.name)>0)
return (child.node.name)
else print("No ajacent node find")
}
# determine active.SeqFrame with selection by the user
# once the mouse clicked on, the SeqFrame.hierachy.view and active.model has to be reset to the selected one
# return selected node name
##########################
#appspace[active.model]=gtkTreeViewGetModel(selection)
## there is only one tree view, but there is multiple dataset SeqFrame serve as node to insert and for plot
## tree view is only for display and interaction with user
## there is multiple view, each action creates one or more views, which has its own data store model
## when add nodes, is the new view automatically created, or has to set every time an action applies to a view
# I think it has to be set again
## determine the active seqSet
## holds some variable/parameters/container in appspace when started, change the state of the parameters when actions are taken
## activeSeqSet
#active.SeqFrame=appspace()
#appspace[activeSeqFrame]=NULL
## just set the selected one to be active, no need for multiple workflow, people can open multiple windows to do that, each window, one workflow
# try change the model of the view when one clicked on the subnodes
# always change model to the corresponding selected nodes name
#active.SeqFrame=
{
# gtkTreeModel for the combo boxes
#channelsModel=rGtkDataFrame(x=)
# channelsXcombo=
# channelsYcombo=
#
#
# channels <- colnames(active.SeqFrame())
#
#
#
#
#
#
# if(channelsDialog$run()==GtkResponseType["ok"]) print("chanel selected")
# channels$destroy()
}
#
#x=PlotPage.data.view$getSelection()
#gtkTreeSelectionGetSelected(x)
## everywhere need a function to referen the selected name to underneath SeqFrame
# return selected node name
# selection=appspace[SeqFrame.hierachy.view]$getSelection()
# iter=gtkTreeSelectionGetSelected(selection)
# model=gtkTreeViewGetModel(appspace[SeqFrame.hierachy.view])
# selected.node.name=model$get(iter=iter$iter,column=0)[[1]]
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