# $Id: mkinGUI.R 122 2013-10-21 20:19:57Z jranke $ {{{1
# gWidgetsWWW2 GUI for mkin
# Copyright (C) 2013 Johannes Ranke
# Contact: jranke@uni-bremen.de, johannesranke@eurofins.com
# This file is part of the R package mkin
# mkin is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software
# Foundation, either version 3 of the License, or (at your option) any later
# version.
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details.
# You should have received a copy of the GNU General Public License along with
# this program. If not, see <http://www.gnu.org/licenses/>
require(mkin) # {{{1
# Set the GUI title and create the basic widget layout {{{1
w <- gwindow("Browser based GUI for kinetic evaluations using mkin")
sb <- gstatusbar("Powered by gWidgetsWWW2 and Rook", cont = w)
pg <- gpanedgroup(cont = w, default.size = 300)
center <- gnotebook(cont = pg)
left <- gvbox(cont = pg)
# Helper functions {{{1
# Override function for making it possible to override original data in the GUI {{{2
override <- function(d) {
data.frame(name = d$name, time = d$time,
value = ifelse(is.na(d$override), d$value, d$override),
err = d$err)
}
# Set default values for project data {{{1
# Initial project file name {{{2
project_file <- "mkin_FOCUS_2006.RData"
# Initial studies {{{2
studies.df <- data.frame(Index = as.integer(1),
Citation = "FOCUS (2006) Guidance on degradation kinetics",
stringsAsFactors = FALSE)
# Initial datasets {{{2
ds <- list()
observed.all <- vector()
for (i in 1:2) {
ds.letter = LETTERS[i + 2]
ds.index <- as.character(i)
ds.name = paste0("FOCUS_2006_", ds.letter)
ds[[ds.index]] <- list(
study_nr = 1,
title = paste("FOCUS example dataset", ds.letter),
sampling_times = unique(get(ds.name)$time),
time_unit = "",
observed = as.character(unique(get(ds.name)$name)),
unit = "% AR",
replicates = 1,
data = get(ds.name)
)
ds[[ds.index]]$data$name <- as.character(ds[[ds.index]]$data$name)
ds[[ds.index]]$data$override = as.numeric(NA)
ds[[ds.index]]$data$err = 1
}
# Dataframe with datasets for selection {{{2
update_ds.df <- function() {
ds.n <- length(ds)
ds.df <<- data.frame(Index = 1:ds.n,
Title = character(ds.n),
Study = character(ds.n),
stringsAsFactors = FALSE)
for (i in 1:ds.n)
{
ds.index <- names(ds)[[i]]
ds.df[i, "Title"] <<- ds[[ds.index]]$title
ds.df[i, "Study"] <<- ds[[ds.index]]$study_nr
observed = as.character(unique(ds[[ds.index]]$data$name))
observed.all <<- union(observed, observed.all)
}
}
ds.df <- data.frame()
update_ds.df()
ds.cur = "1"
# Initial models {{{2
m <- list()
m[["1"]] <- mkinmod(parent = list(type = "SFO"))
m[["1"]]$name = "SFO"
m[["2"]] <- mkinmod(parent = list(type = "FOMC"))
m[["2"]]$name = "FOMC"
m[["3"]] <- mkinmod(parent = list(type = "DFOP"))
m[["3"]]$name = "DFOP"
m[["4"]] <- mkinmod(parent = list(type = "SFO", to = "m1"),
m1 = list(type = "SFO"),
use_of_ff = "max")
m[["4"]]$name = "SFO_SFO"
# Dataframe with models for selection {{{2
update_m.df <- function() {
m.n <- length(m)
m.df <<- data.frame(Index = 1:m.n,
Name = character(m.n),
stringsAsFactors = FALSE)
for (i in 1:m.n) {
m.index <- names(m)[[i]]
m.df[i, "Name"] <<- m[[m.index]]$name
}
}
m.df <- data.frame()
update_m.df()
m.cur = "1"
# Initial fit lists {{{2
# The fits and summaries are collected in lists of lists
f <- s <- list()
for (ds.index in 1:length(ds)) {
f[[as.character(ds.index)]] <- list()
s[[as.character(ds.index)]] <- list()
}
f[["1"]][["1"]] <- suppressWarnings(mkinfit(m[["1"]], override(ds[["1"]]$data),
err = "err",
control.modFit = list(maxiter = 0)))
# Widgets and handlers for project data {{{1
prg <- gexpandgroup("Project file management", cont = left, horizontal = FALSE)
# Project data management handler functions {{{2
upload_file_handler <- function(h, ...)
{
tmpfile <- normalizePath(svalue(h$obj), winslash = "/")
try(load(tmpfile))
project_file <<- pr.gf$filename
svalue(pr.ge) <- project_file
studies.gdf[,] <- studies.df
ds.cur <<- "1"
ds <<- ds
update_ds.df()
ds.gtable[,] <- ds.df
update_ds_editor()
m.cur <<- "1"
m <<- m
update_m.df()
m.gtable[,] <- m.df
update_m_editor()
}
save_to_file_handler <- function(h, ...)
{
studies.df <- data.frame(studies.gdf[,], stringsAsFactors = FALSE)
save(studies.df, ds, m, file = project_file)
galert(paste("Saved project contents to", project_file), parent = w)
}
change_project_file_handler = function(h, ...) {
project_file <<- as.character(svalue(h$obj))
}
# Project data management GUI elements {{{2
pr.gf <- gfile(text = "Select project file", cont = prg,
handler = upload_file_handler)
pr.ge <- gedit(project_file, cont = prg,
handler = change_project_file_handler)
# The save button is always visible {{{1
gbutton("Save current project contents", cont = left,
handler = save_to_file_handler)
# GUI widgets and a function for Studies {{{1
stg <- gexpandgroup("Studies", cont = left)
visible(stg) <- FALSE
update_study_selector <- function(h, ...) {
delete(ds.e.1, ds.study.gc)
ds.study.gc <<- gcombobox(paste("Study", studies.gdf[,1]), cont = ds.e.1)
svalue(ds.study.gc, index = TRUE) <- ds[[ds.cur]]$study_nr
}
studies.gdf <- gdf(studies.df, name = "Edit studies in the project",
width = 290, height = 200, cont = stg)
studies.gdf$set_column_width(1, 40)
studies.gdf$set_column_width(2, 240)
addHandlerChanged(studies.gdf, update_study_selector)
# Datasets and models {{{1
dsm <- gframe("Datasets and models", cont = left, horizontal = FALSE)
# Dataset table with handler {{{2
ds.switcher <- function(h, ...) {
ds.cur <<- as.character(svalue(h$obj))
update_ds_editor()
svalue(center) <- 1
}
ds.gtable <- gtable(ds.df, width = 290, cont = dsm)
addHandlerDoubleClick(ds.gtable, ds.switcher)
size(ds.gtable) <- list(columnWidths = c(40, 200, 40))
ds.gtable$value <- 1
# Model table with handler {{{2
m.switcher <- function(h, ...) {
m.cur <<- as.character(svalue(h$obj))
update_m_editor()
svalue(center) <- 2
}
m.gtable <- gtable(m.df, width = 290, cont = dsm)
addHandlerDoubleClick(m.gtable, m.switcher)
size(m.gtable) <- list(columnWidths = c(40, 240))
m.gtable$value <- 1
# Button for setting up a fit for the selected dataset and model
gbutton("Configure fit for selected model and dataset", cont = dsm,
handler = function(h, ...) {
ds.i <<- svalue(ds.gtable)
m.i <<- svalue(m.gtable)
f[[ds.i]][[m.i]] <<- suppressWarnings(
mkinfit(m[[m.i]], override(ds[[ds.i]]$data),
err = "err",
control.modFit = list(maxiter = 0)))
stmp <- summary(f[[ds.i]][[m.i]])
f.gg.parms[,] <- get_Parameters(stmp, FALSE)
show_plot("Initial", default = TRUE)
svalue(pf) <- paste0("Dataset ", ds.i, ", Model ", m.i)
svalue(center) <- 3
})
# Dataset editor {{{1
ds.editor <- gframe("Dataset 1", horizontal = FALSE, cont = center, label = "Dataset editor")
# Handler functions {{{3
copy_dataset_handler <- function(h, ...) {
ds.old <- ds.cur
ds.cur <<- as.character(1 + length(ds))
svalue(ds.editor) <- paste("Dataset", ds.cur)
ds[[ds.cur]] <<- ds[[ds.old]]
update_ds.df()
ds.gtable[,] <- ds.df
}
delete_dataset_handler <- function(h, ...) {
ds[[ds.cur]] <<- NULL
names(ds) <<- names(plots) <<- names(prows) <<- as.character(1:length(ds))
ds.cur <<- names(ds)[[1]]
update_ds.df()
ds.gtable[,] <- ds.df
update_ds_editor()
}
new_dataset_handler <- function(h, ...) {
ds.cur <<- as.character(1 + length(ds))
ds[[ds.cur]] <<- list(
study_nr = 1,
title = "",
sampling_times = c(0, 1),
time_unit = "NA",
observed = "parent",
unit = "NA",
replicates = 1,
data = data.frame(
name = "parent",
time = c(0, 1),
value = c(100, NA),
override = "NA",
err = 1,
stringsAsFactors = FALSE
)
)
update_ds.df()
ds.gtable[,] <- ds.df
update_ds_editor()
}
empty_grid_handler <- function(h, ...) {
obs <- strsplit(svalue(ds.e.obs), ", ")[[1]]
sampling_times <- strsplit(svalue(ds.e.st), ", ")[[1]]
replicates <- as.numeric(svalue(ds.e.rep))
new.data = data.frame(
name = rep(obs, each = replicates * length(sampling_times)),
time = rep(sampling_times, each = replicates, times = length(obs)),
value = NA,
override = NA,
err = 1
)
ds.e.gdf[,] <- new.data
}
save_ds_changes_handler <- function(h, ...) {
ds[[ds.cur]]$title <<- svalue(ds.title.ge)
ds[[ds.cur]]$study_nr <<- as.numeric(gsub("Study ", "", svalue(ds.study.gc)))
update_ds.df()
ds.gtable[,] <- ds.df
tmpd <- ds.e.gdf[,]
ds[[ds.cur]]$data <<- tmpd
ds[[ds.cur]]$sampling_times <<- sort(unique(tmpd$time))
ds[[ds.cur]]$time_unit <<- svalue(ds.e.stu)
ds[[ds.cur]]$observed <<- unique(tmpd$name)
ds[[ds.cur]]$unit <<- svalue(ds.e.obu)
ds[[ds.cur]]$replicates <<- max(aggregate(tmpd$time,
list(tmpd$time, tmpd$name), length)$x)
update_ds_editor()
}
# Widget setup {{{3
# Line 1 {{{4
ds.e.1 <- ggroup(cont = ds.editor, horizontal = TRUE)
glabel("Title: ", cont = ds.e.1)
ds.title.ge <- gedit(ds[[ds.cur]]$title, cont = ds.e.1)
glabel(" from ", cont = ds.e.1)
ds.study.gc <- gcombobox(paste("Study", studies.gdf[,1]), cont = ds.e.1)
# Line 2 {{{4
ds.e.2 <- ggroup(cont = ds.editor, horizontal = TRUE)
gbutton("Copy dataset", cont = ds.e.2, handler = copy_dataset_handler)
gbutton("Delete dataset", cont = ds.e.2, handler = delete_dataset_handler)
gbutton("New dataset", cont = ds.e.2, handler = new_dataset_handler)
# Line 3 with forms {{{4
ds.e.forms <- ggroup(cont= ds.editor, horizontal = TRUE)
ds.e.3a <- gvbox(cont = ds.e.forms)
ds.e.3a.gfl <- gformlayout(cont = ds.e.3a)
ds.e.st <- gedit(paste(ds[[ds.cur]]$sampling_times, collapse = ", "),
width = 40,
label = "Sampling times",
cont = ds.e.3a.gfl)
ds.e.stu <- gedit(ds[[ds.cur]]$time_unit,
width = 20,
label = "Unit", cont = ds.e.3a.gfl)
ds.e.rep <- gedit(ds[[ds.cur]]$replicates,
width = 20,
label = "Replicates", cont = ds.e.3a.gfl)
ds.e.3b <- gvbox(cont = ds.e.forms)
ds.e.3b.gfl <- gformlayout(cont = ds.e.3b)
ds.e.obs <- gedit(paste(ds[[ds.cur]]$observed, collapse = ", "),
width = 50,
label = "Observed", cont = ds.e.3b.gfl)
ds.e.obu <- gedit(ds[[ds.cur]]$unit,
width = 20, label = "Unit",
cont = ds.e.3b.gfl)
gbutton("Generate empty grid for kinetic data", cont = ds.e.3b,
handler = empty_grid_handler)
# Save button {{{4
gbutton("Save changes", cont = ds.editor, handler = save_ds_changes_handler)
# Kinetic Data {{{4
ds.e.gdf <- gdf(ds[[ds.cur]]$data, name = "Kinetic data",
width = 500, height = 700, cont = ds.editor)
ds.e.gdf$set_column_width(2, 70)
# Update the dataset editor {{{3
update_ds_editor <- function() {
svalue(ds.editor) <- paste("Dataset", ds.cur)
svalue(ds.title.ge) <- ds[[ds.cur]]$title
svalue(ds.study.gc, index = TRUE) <- ds[[ds.cur]]$study_nr
svalue(ds.e.st) <- paste(ds[[ds.cur]]$sampling_times, collapse = ", ")
svalue(ds.e.stu) <- ds[[ds.cur]]$time_unit
svalue(ds.e.obs) <- paste(ds[[ds.cur]]$observed, collapse = ", ")
svalue(ds.e.obu) <- ds[[ds.cur]]$unit
svalue(ds.e.rep) <- ds[[ds.cur]]$replicates
ds.e.gdf[,] <- ds[[ds.cur]]$data
}
# Model editor {{{1
m.editor <- gframe("Model 1", horizontal = FALSE, cont = center, label = "Model editor")
# Handler functions {{{3
copy_model_handler <- function(h, ...) {
m.old <- m.cur
m.cur <<- as.character(1 + length(m))
svalue(m.editor) <- paste("Model", m.cur)
m[[m.cur]] <<- m[[m.old]]
update_m.df()
m.gtable[,] <- m.df
}
delete_model_handler <- function(h, ...) {
m[[m.cur]] <<- NULL
names(m) <<- as.character(1:length(m))
m.cur <<- "1"
update_m.df()
m.gtable[,] <- m.df
update_m_editor()
}
add_observed_handler <- function(h, ...) {
obs.i <- length(m.e.rows) + 1
m.e.rows[[obs.i]] <<- ggroup(cont = m.editor, horizontal = TRUE)
m.e.obs[[obs.i]] <<- gcombobox(observed.all, selected = obs.i,
cont = m.e.rows[[obs.i]])
m.e.type[[obs.i]] <<- gcombobox(c("SFO", "FOMC", "DFOP", "HS", "SFORB"),
cont = m.e.rows[[obs.i]])
svalue(m.e.type[[obs.i]]) <- "SFO"
glabel("to", cont = m.e.rows[[obs.i]])
m.e.to[[obs.i]] <<- gedit("", cont = m.e.rows[[obs.i]])
m.e.sink[[obs.i]] <<- gcheckbox("Path to sink",
checked = TRUE, cont = m.e.rows[[obs.i]])
gbutton("Remove compound", handler = remove_compound_handler,
action = obs.i, cont = m.e.rows[[obs.i]])
}
remove_compound_handler <- function(h, ...) {
m[[m.cur]]$spec[[h$action]] <<- NULL
update_m_editor()
}
save_m_changes_handler <- function(h, ...) {
spec <- list()
for (obs.i in 1:length(m.e.rows)) {
spec[[obs.i]] <- list(type = svalue(m.e.type[[obs.i]]),
to = svalue(m.e.to[[obs.i]]),
sink = svalue(m.e.sink[[obs.i]]))
if(spec[[obs.i]]$to == "") spec[[obs.i]]$to = NULL
names(spec)[[obs.i]] <- svalue(m.e.obs[[obs.i]])
}
m[[m.cur]] <<- mkinmod(use_of_ff = svalue(m.ff.gc),
speclist = spec)
m[[m.cur]]$name <<- svalue(m.name.ge)
update_m.df()
m.gtable[,] <- m.df
}
# Widget setup {{{3
m.e.0 <- ggroup(cont = m.editor, horizontal = TRUE)
glabel("Model name: ", cont = m.e.0)
m.name.ge <- gedit(m[[m.cur]]$name, cont = m.e.0)
glabel("Use of formation fractions: ", cont = m.e.0)
m.ff.gc <- gcombobox(c("min", "max"), cont = m.e.0)
svalue(m.ff.gc) <- m[[m.cur]]$use_of_ff
# Model handling buttons {{{4
m.e.b <- ggroup(cont = m.editor, horizontal = TRUE)
gbutton("Copy model", cont = m.e.b, handler = copy_model_handler)
gbutton("Delete model", cont = m.e.b, handler = delete_model_handler)
gbutton("Add transformation product", cont = m.e.b,
handler = add_observed_handler)
gbutton("Save changes", cont = m.e.b, handler = save_m_changes_handler)
m.observed <- names(m[[m.cur]]$spec)
m.e.rows <- m.e.obs <- m.e.type <- m.e.to <- m.e.sink <- list()
obs.to <- ""
# Show the model specification {{{4
show_m_spec <- function() {
for (obs.i in 1:length(m.observed)) {
m.e.rows[[obs.i]] <<- ggroup(cont = m.editor, horizontal = TRUE)
m.e.obs[[obs.i]] <<- gcombobox(observed.all, selected = obs.i,
cont = m.e.rows[[obs.i]])
m.e.type[[obs.i]] <<- gcombobox(c("SFO", "FOMC", "DFOP", "HS", "SFORB"),
cont = m.e.rows[[obs.i]])
svalue(m.e.type[[obs.i]]) <<- m[[m.cur]]$spec[[obs.i]]$type
glabel("to", cont = m.e.rows[[obs.i]])
obs.to <<- ifelse(is.null(m[[m.cur]]$spec[[obs.i]]$to), "",
m[[m.cur]]$spec[[obs.i]]$to)
m.e.to[[obs.i]] <<- gedit(obs.to, cont = m.e.rows[[obs.i]])
m.e.sink[[obs.i]] <<- gcheckbox("Path to sink", checked = m[[m.cur]]$spec[[obs.i]]$sink,
cont = m.e.rows[[obs.i]])
if (obs.i > 1) {
gbutton("Remove compound", handler = remove_compound_handler,
action = obs.i, cont = m.e.rows[[obs.i]])
}
}
}
show_m_spec()
# Update the model editor {{{3
update_m_editor <- function() {
svalue(m.editor) <- paste("Model", m.cur)
svalue(m.name.ge) <- m[[m.cur]]$name
svalue(m.ff.gc) <- m[[m.cur]]$use_of_ff
for (oldrow.i in 1:length(m.e.rows)) {
delete(m.editor, m.e.rows[[oldrow.i]])
}
m.observed <<- names(m[[m.cur]]$spec)
m.e.rows <<- m.e.obs <<- m.e.type <<- m.e.to <<- m.e.sink <<- list()
show_m_spec()
}
# 3}}}
# 2}}}
# Plotting and fitting {{{1
show_plot <- function(type, default = FALSE) {
Parameters <- f.gg.parms[,]
Parameters.de <- subset(Parameters, Type == "deparm", type)
stateparms <- subset(Parameters, Type == "state")[[type]]
deparms <- as.numeric(Parameters.de[[type]])
names(deparms) <- rownames(Parameters.de)
if (type == "Initial" & default == FALSE) {
f[[ds.i]][[m.i]] <<- suppressWarnings(
mkinfit(m[[m.i]], override(ds[[ds.i]]$data),
state.ini = stateparms, parms.ini = deparms,
err = "err",
control.modFit = list(maxiter = 0))
)
}
tmp <- get_tempfile(ext=".svg")
svg(tmp, width = 7, height = 5)
plot(f[[ds.i]][[m.i]], main = ds[[ds.i]]$title,
xlab = ifelse(ds[[ds.i]]$time_unit == "", "Time",
paste("Time in", ds[[ds.i]]$time_unit)),
ylab = ifelse(ds[[ds.i]]$unit == "", "Observed",
paste("Observed in", ds[[ds.i]]$unit)))
dev.off()
svalue(plot.gs) <<- tmp
}
get_Parameters <- function(stmp, optimised)
{
pars <- rbind(stmp$start[1:2], stmp$fixed)
pars$fixed <- c(rep(FALSE, length(stmp$start$value)),
rep(TRUE, length(stmp$fixed$value)))
pars$name <- rownames(pars)
Parameters <- data.frame(Name = pars$name,
Type = pars$type,
Initial = pars$value,
Fixed = pars$fixed,
Optimised = as.numeric(NA))
Parameters <- rbind(subset(Parameters, Type == "state"),
subset(Parameters, Type == "deparm"))
rownames(Parameters) <- Parameters$Name
if (optimised) {
Parameters[rownames(stmp$bpar), "Optimised"] <- stmp$bpar[, "Estimate"]
}
return(Parameters)
}
run_fit <- function() {
Parameters <- f.gg.parms[,]
Parameters.de <- subset(Parameters, Type == "deparm")
deparms <- Parameters.de$Initial
names(deparms) <- rownames(Parameters.de)
f[[ds.i]][[m.i]] <<- mkinfit(m[[m.i]], override(ds[[ds.i]]$data),
state.ini = subset(Parameters,
Type == "state")$Initial,
parms.ini = deparms,
err = "err")
s[[ds.i]][[m.i]] <<- summary(f[[ds.i]][[m.i]])
f.gg.parms[,] <- get_Parameters(s[[ds.i]][[m.i]], TRUE)
show_plot("Optimised")
}
ds.i <- m.i <- "1"
# GUI widgets {{{2
pf <- gframe("Dataset 1, Model 1", horizontal = FALSE,
cont = center, label = "Plotting and fitting")
# Head row with buttons {{{3
f.gg.head <- ggroup(cont = pf)
gbutton("Show initial",
handler = function(h, ...) show_plot("Initial"),
cont = f.gg.head)
gbutton("Run", handler = function(h, ...) run_fit(),
cont = f.gg.head)
# Mid group with plot and options
f.gg.mid <- ggroup(cont = pf)
stmp <- summary(f[["1"]][["1"]])
Parameters <- get_Parameters(stmp, FALSE)
tf <- get_tempfile(ext=".svg")
svg(tf, width = 7, height = 5)
plot(f[["1"]][["1"]])
dev.off()
plot.gs <- gsvg(tf, container = f.gg.mid, width = 490, height = 350)
f.gg.opts <- gformlayout(cont = f.gg.mid)
solution_types <- c("analytical", "eigen", "deSolve")
gcombobox(solution_types, selected = 1, label = "solution_type",
width = 200, cont = f.gg.opts)
# Dataframe with initial and optimised parameters
f.gg.parms <- gdf(Parameters, width = 420, height = 300, cont = pf,
do_add_remove_buttons = FALSE)
f.gg.parms$set_column_width(1, 200)
f.gg.parms$set_column_width(2, 50)
f.gg.parms$set_column_width(3, 60)
f.gg.parms$set_column_width(4, 50)
f.gg.parms$set_column_width(5, 60)
# 1}}}
# vim: set foldmethod=marker ts=2 sw=2 expandtab:
