From 66620036c4943c03072b113a63fcd983390102b8 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 18 Nov 2013 20:13:58 +0100 Subject: Add GUI start function, keep GUI here in mkin --- inst/GUI/gmkin.R | 826 +++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 826 insertions(+) create mode 100644 inst/GUI/gmkin.R (limited to 'inst/GUI/gmkin.R') diff --git a/inst/GUI/gmkin.R b/inst/GUI/gmkin.R new file mode 100644 index 00000000..07f892e0 --- /dev/null +++ b/inst/GUI/gmkin.R @@ -0,0 +1,826 @@ +# $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 +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]]$name + } +} +m.df <- data.frame() +update_m.df() +m.cur = "1" +# Initial fit lists {{{2 +# The fits and summaries are collected in lists of lists +f <- s <- list() +# Dataframe with fits for selection {{{2 +update_f.df <- function() { + f.df <<- data.frame(Fit = character(), + Dataset = character(), + Model = character(), + stringsAsFactors = FALSE) + f.count <- 0 + for (fit.index in names(f)) { + f.count <- f.count + 1 + ftmp <- f[[fit.index]] + f.df[f.count, ] <<- c(as.character(f.count), ftmp$ds.index, ftmp$mkinmod$name) + } +} +f.df.empty <- f.df <- data.frame(Fit = "0", + Dataset = "", + Model = "", + stringsAsFactors = FALSE) +# 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, ...) +{ + # General + tmpfile <- normalizePath(svalue(h$obj), winslash = "/") + try(load(tmpfile)) + project_file <<- pr.gf$filename + svalue(pr.ge) <- project_file + + # Studies + studies.gdf[,] <- studies.df + + # Datasets + ds.cur <<- ds.cur + ds <<- ds + update_ds.df() + ds.gtable[,] <- ds.df + update_ds_editor() + + # Models + m.cur <<- ds.cur + m <<- m + update_m.df() + m.gtable[,] <- m.df + update_m_editor() + + # Fits + f.cur <<- f.cur + f <<- f + s <<- s + if (length(f) > 0) update_f.df() + else f.df <- f.df.empty + f.gtable[,] <- f.df + ftmp <<- f[[f.cur]] + stmp <<- s[[f.cur]] + ds.i <<- ds.cur + update_plotting_and_fitting() +} +save_to_file_handler <- function(h, ...) +{ + studies.df <- data.frame(studies.gdf[,], stringsAsFactors = FALSE) + save(studies.df, ds, ds.cur, m, m.cur, f, s, f.cur, 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 <<- as.character(svalue(ds.gtable)) + m.i <<- as.character(svalue(m.gtable)) + ftmp <<- suppressWarnings(mkinfit(m[[m.i]], + override(ds[[ds.i]]$data), + err = "err", + control.modFit = list(maxiter = 0))) + ftmp$ds.index <<- ds.i + ftmp$ds <<- ds[[ds.i]] + stmp <<- summary(ftmp) + svalue(pf) <- paste0("Dataset ", ds.i, ", Model ", m[[m.i]]$name) + show_plot("Initial", default = TRUE) + svalue(f.gg.opts.st) <<- ftmp$solution_type + svalue(f.gg.opts.weight) <<- ftmp$weight + svalue(f.gg.opts.atol) <<- ftmp$atol + svalue(f.gg.opts.rtol) <<- ftmp$rtol + svalue(f.gg.opts.reweight.method) <<- ifelse( + is.null(ftmp$reweight.method), + "none", ftmp$reweight.method) + svalue(f.gg.opts.reweight.tol) <<- ftmp$reweight.tol + svalue(f.gg.opts.reweight.max.iter) <<- ftmp$reweight.max.iter + f.gg.parms[,] <- get_Parameters(stmp, FALSE) + svalue(f.gg.summary) <- capture.output(stmp) + svalue(center) <- 3 + }) + +# Fits {{{1 +f.gf <- gframe("Fits", cont = left, horizontal = FALSE) +# Fit table with handler {{{2 +f.switcher <- function(h, ...) { + if (svalue(h$obj) != "0") { + f.cur <<- svalue(h$obj) + ftmp <<- f[[f.cur]] + stmp <<- s[[f.cur]] + ds.i <<- ftmp$ds.index + update_plotting_and_fitting() + } + svalue(center) <- 3 +} +f.gtable <- gtable(f.df, width = 290, cont = f.gf) +addHandlerDoubleClick(f.gtable, f.switcher) +size(f.gtable) <- list(columnWidths = c(40, 60, 180)) + +# Dataset editor {{{1 +ds.editor <- gframe("Dataset 1", horizontal = FALSE, cont = center, label = "Dataset editor") +# Handler functions {{{3 +copy_dataset_handler <- function(h, ...) { + ds.old <- ds.cur + ds.cur <<- as.character(1 + length(ds)) + svalue(ds.editor) <- paste("Dataset", ds.cur) + ds[[ds.cur]] <<- ds[[ds.old]] + update_ds.df() + ds.gtable[,] <- ds.df +} + +delete_dataset_handler <- function(h, ...) { + ds[[ds.cur]] <<- NULL + names(ds) <<- as.character(1:length(ds)) + ds.cur <<- names(ds)[[1]] + update_ds.df() + ds.gtable[,] <- ds.df + update_ds_editor() +} + +new_dataset_handler <- function(h, ...) { + ds.cur <<- as.character(1 + length(ds)) + ds[[ds.cur]] <<- list( + study_nr = 1, + title = "", + sampling_times = c(0, 1), + time_unit = "", + observed = "parent", + unit = "", + replicates = 1, + data = data.frame( + name = "parent", + time = c(0, 1), + value = c(100, NA), + override = "NA", + err = 1, + stringsAsFactors = FALSE + ) + ) + update_ds.df() + ds.gtable[,] <- ds.df + update_ds_editor() +} + +new_ds_from_csv_handler <- function(h, ...) { + tmpfile <- normalizePath(svalue(h$obj), winslash = "/") + tmpd <- try(read.table(tmpfile, sep = "\t", header = TRUE, stringsAsFactors = FALSE)) + tmpdw <- mkin_wide_to_long(tmpd) + if (class(tmpd) != "try-error") { + ds.cur <<- as.character(1 + length(ds)) + ds[[ds.cur]] <<- list( + study_nr = NA, + title = "New upload", + sampling_times = sort(unique(tmpd$t)), + time_unit = "", + observed = unique(tmpdw$name), + unit = "", + replicates = max(aggregate(tmpdw$time, + list(tmpdw$time, + tmpdw$name), + length)$x), + data = tmpdw) + ds[[ds.cur]]$data$override <<- as.numeric(NA) + ds[[ds.cur]]$data$err <<- 1 + update_ds.df() + ds.gtable[,] <- ds.df + update_ds_editor() + } else { + galert("Uploading failed", parent = "w") + } +} + +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 = as.numeric(rep(sampling_times, each = replicates, times = length(obs))), + value = as.numeric(NA), + override = as.numeric(NA), + err = 1, + stringsAsFactors = FALSE + ) + ds.e.gdf[,] <- new.data +} + +keep_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]]$title, cont = ds.e.1) +glabel(" from ", cont = ds.e.1) +ds.study.gc <- gcombobox(paste("Study", studies.gdf[,1]), cont = ds.e.1) + +# Line 2 {{{4 +ds.e.2 <- ggroup(cont = ds.editor, horizontal = TRUE) +gbutton("Copy dataset", cont = ds.e.2, handler = copy_dataset_handler) +gbutton("Delete dataset", cont = ds.e.2, handler = delete_dataset_handler) +gbutton("New dataset", cont = ds.e.2, handler = new_dataset_handler) + +upload_dataset.gf <- gfile(text = "Upload text file", cont = ds.e.2, + handler = new_ds_from_csv_handler) + +# Line 3 with forms {{{4 +ds.e.forms <- ggroup(cont= ds.editor, horizontal = TRUE) + +ds.e.3a <- gvbox(cont = ds.e.forms) +ds.e.3a.gfl <- gformlayout(cont = ds.e.3a) +ds.e.st <- gedit(paste(ds[[ds.cur]]$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) +generate_grid.gb <- gbutton("Generate empty grid for kinetic data", cont = ds.e.3b, + handler = empty_grid_handler) +tooltip(generate_grid.gb) <- "Overwrites the kinetic data shown below" + +# Keep button {{{4 +gbutton("Keep changes", cont = ds.editor, handler = keep_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() +} + +keep_m_changes_handler <- function(h, ...) { + spec <- list() + for (obs.i in 1:length(m.e.rows)) { + to_vector = strsplit(svalue(m.e.to[[obs.i]]), ", ")[[1]] + if (length(to_vector) == 0) to_vector = "" + spec[[obs.i]] <- list(type = svalue(m.e.type[[obs.i]]), + to = to_vector, + 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]]$use_of_ff + +# Model handling buttons {{{4 +m.e.b <- ggroup(cont = m.editor, horizontal = TRUE) +gbutton("Copy model", cont = m.e.b, handler = copy_model_handler) +gbutton("Delete model", cont = m.e.b, handler = delete_model_handler) +gbutton("Add transformation product", cont = m.e.b, + handler = add_observed_handler) +gbutton("Keep changes", cont = m.e.b, handler = keep_m_changes_handler) + + +m.observed <- names(m[[m.cur]]$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[[m.cur]]$spec)) { + obs.name <- names(m[[m.cur]]$spec)[[obs.i]] + m.e.rows[[obs.i]] <<- ggroup(cont = m.editor, horizontal = TRUE) + m.e.obs[[obs.i]] <<- gcombobox(observed.all, selected = 0, + cont = m.e.rows[[obs.i]]) + svalue(m.e.obs[[obs.i]]) <<- obs.name + 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), "", + paste(m[[m.cur]]$spec[[obs.i]]$to, collapse = ", ")) + 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]]$spec) + m.e.rows <<- m.e.obs <<- m.e.type <<- m.e.to <<- m.e.sink <<- list() + show_m_spec() +} + +# 3}}} +# 2}}} +# Plotting and fitting {{{1 +show_plot <- function(type, default = FALSE) { + Parameters <- f.gg.parms[,] + Parameters.de <- subset(Parameters, Type == "deparm", type) + stateparms <- subset(Parameters, Type == "state")[[type]] + deparms <- as.numeric(Parameters.de[[type]]) + names(deparms) <- rownames(Parameters.de) + if (type == "Initial" & default == FALSE) { + ftmp <<- suppressWarnings(mkinfit(ftmp$mkinmod, + override(ds[[ds.i]]$data), + state.ini = stateparms, + parms.ini = deparms, + err = "err", + control.modFit = list(maxiter = 0))) + ftmp$ds.index <<- ds.i + ftmp$ds <<- ds[[ds.i]] + } + + svg(tf, width = 7, height = 5) + plot(ftmp, main = ftmp$ds$title, + xlab = ifelse(ftmp$ds$time_unit == "", "Time", + paste("Time in", ftmp$ds$time_unit)), + ylab = ifelse(ds[[ds.i]]$unit == "", "Observed", + paste("Observed in", ftmp$ds$unit))) + dev.off() + svalue(plot.gs) <<- tf +} +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) <- Parameters.de$Name + defixed <- names(deparms[Parameters.de$Fixed]) + Parameters.ini <- subset(Parameters, Type == "state") + iniparms <- Parameters.ini$Initial + names(iniparms) <- sub("_0", "", Parameters.ini$Name) + inifixed <- names(iniparms[Parameters.ini$Fixed]) + weight <- svalue(f.gg.opts.weight) + if (weight == "manual") { + err = "err" + } else { + err = NULL + } + reweight.method <- svalue(f.gg.opts.reweight.method) + if (reweight.method == "none") reweight.method = NULL + ftmp <<- mkinfit(ftmp$mkinmod, override(ds[[ds.i]]$data), + state.ini = iniparms, + fixed_initials = inifixed, + parms.ini = deparms, + fixed_parms = defixed, + solution_type = svalue(f.gg.opts.st), + atol = as.numeric(svalue(f.gg.opts.atol)), + rtol = as.numeric(svalue(f.gg.opts.rtol)), + weight = weight, + err = err, + reweight.method = reweight.method, + reweight.tol = as.numeric(svalue(f.gg.opts.reweight.tol)), + reweight.max.iter = as.numeric(svalue(f.gg.opts.reweight.max.iter)) + ) + ftmp$ds.index <<- ds.i + ftmp$ds <<- ds[[ds.i]] + stmp <<- summary(ftmp) + show_plot("Optimised") + svalue(f.gg.opts.st) <- ftmp$solution_type + svalue(f.gg.opts.weight) <- ftmp$weight.ini + f.gg.parms[,] <- get_Parameters(stmp, TRUE) + svalue(f.gg.summary) <- capture.output(stmp) +} +ds.i <- m.i <- "1" +f.cur <- "0" + +# GUI widgets {{{2 +pf <- gframe("Dataset 1, Model SFO", horizontal = FALSE, + cont = center, label = "Plotting and fitting") + +# Mid group with plot and options {{{3 +f.gg.mid <- ggroup(cont = pf) +ftmp <- suppressWarnings(mkinfit(m[[m.cur]], override(ds[[ds.i]]$data), + err = "err", + control.modFit = list(maxiter = 0))) +ftmp$ds.index = ds.i +ftmp$ds = ds[[ds.i]] +stmp <- summary(ftmp) +Parameters <- get_Parameters(stmp, FALSE) +tf <- get_tempfile(ext=".svg") +svg(tf, width = 7, height = 5) +plot(ftmp) +dev.off() +plot.gs <- gsvg(tf, container = f.gg.mid, width = 420, height = 300) +f.gg.opts <- gformlayout(cont = f.gg.mid) +solution_types <- c("auto", "analytical", "eigen", "deSolve") +f.gg.opts.st <- gcombobox(solution_types, selected = 1, + label = "solution_type", width = 200, + cont = f.gg.opts) +f.gg.opts.atol <- gedit(ftmp$atol, label = "atol", width = 20, + cont = f.gg.opts) +f.gg.opts.rtol <- gedit(ftmp$rtol, label = "rtol", width = 20, + cont = f.gg.opts) +weights <- c("manual", "none", "std", "mean") +f.gg.opts.weight <- gcombobox(weights, selected = 1, label = "weight", + width = 200, cont = f.gg.opts) +f.gg.opts.reweight.method <- gcombobox(c("none", "obs"), selected = 1, + label = "reweight.method", + width = 200, + cont = f.gg.opts) +f.gg.opts.reweight.tol <- gedit(1e-8, label = "reweight.tol", + width = 20, cont = f.gg.opts) +f.gg.opts.reweight.max.iter <- gedit(10, label = "reweight.max.iter", + width = 20, cont = f.gg.opts) + +# Dataframe with initial and optimised parameters {{{3 +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$set_column_width(5, 60) + +# Row with buttons {{{3 +f.gg.buttons <- ggroup(cont = pf) +show.initial.gb <- gbutton("Show initial", + handler = function(h, ...) show_plot("Initial"), + cont = f.gg.buttons) +tooltip(show.initial.gb) <- "Show model with current inital settings for current dataset" +run.fit.gb <- gbutton("Run", + handler = function(h, ...) run_fit(), cont = + f.gg.buttons) +tooltip(run.fit.gb) <- "Fit with current settings on the current dataset, with the original model" +keep.fit.gb <- gbutton("Keep", + handler = function(h, ...) { + f.cur <<- as.character(length(f) + 1) + f[[f.cur]] <<- ftmp + s[[f.cur]] <<- stmp + update_f.df() + f.gtable[,] <<- f.df + }, cont = f.gg.buttons) +tooltip(keep.fit.gb) <- "Store the optimised model with all settings and the current dataset in the fit list" + +show.plots.gb <- gbutton("Show plots", + handler = function(h, ...) show_plot_window(), + cont = f.gg.buttons) +tooltip(show.plots.gb) <- "Show a window with plots including residual plots" + +# Summary {{{3 +f.gg.summary <- gtext(capture.output(stmp), cont = pf, + use.codemirror = TRUE) + + +delete.fit.gb <- gbutton("Delete", handler = function(h, ...) { + if (length(f) > 0) { + f[[f.cur]] <<- NULL + s[[f.cur]] <<- NULL + } + if (length(f) > 0) { + names(f) <<- as.character(1:length(f)) + names(s) <<- as.character(1:length(f)) + update_f.df() + f.cur <<- "1" + ftmp <<- f[[f.cur]] + stmp <<- s[[f.cur]] + ds.i <<- ftmp$ds.index + update_plotting_and_fitting() + } else { + f.df <<- f.df.empty + f.cur <<- "0" + } + f.gtable[,] <<- f.df + }, cont = f.gg.buttons) +tooltip(delete.fit.gb) <- "Delete the currently loaded fit from the fit list" + +# Update the plotting and fitting area {{{3 +update_plotting_and_fitting <- function() { + svalue(pf) <- paste0("Fit ", f.cur, ": Dataset ", ftmp$ds.index, + ", Model ", ftmp$mkinmod$name) + show_plot("Optimised") + svalue(f.gg.opts.st) <- ftmp$solution_type + svalue(f.gg.opts.weight) <- ftmp$weight.ini + svalue(f.gg.opts.reweight.method) <- ifelse(is.null(ftmp$reweight.method), + "none", + ftmp$reweight.method) + svalue(f.gg.opts.reweight.tol) <- ftmp$reweight.tol + svalue(f.gg.opts.reweight.max.iter) <- ftmp$reweight.max.iter + f.gg.parms[,] <- get_Parameters(stmp, TRUE) + svalue(f.gg.summary) <- capture.output(stmp) +} + +# Show plot window with residual plots {{{3 +show_plot_window <- function(h, ...) { + n.obs = length(ftmp$mkinmod$spec) + obs.vars = names(ftmp$mkinmod$spec) + parent = obs.vars[1] + if(n.obs == 1) { + n.rows = 1 + ps = 7 + } else { + n.rows = 1 + ceiling(n.obs / 2) + ps = 10 + } + imgwidth = 800 + imgheight = 360 * n.rows + pw <- gwindow("Plot window", parent = w, + width = imgwidth + 20, height = imgheight + 100) + pwg <- ggroup(cont = pw, horizontal = FALSE) + make_plots <- function() { + par(mfrow = c(n.rows, 2)) + plot(ftmp, main = ftmp$ds$title, + xlab = ifelse(ftmp$ds$time_unit == "", "Time", + paste("Time in", ftmp$ds$time_unit)), + ylab = ifelse(ds[[ds.i]]$unit == "", "Observed", + paste("Observed in", ftmp$ds$unit))) + if (n.obs > 1) { + plot(ftmp, legend = FALSE, + main = paste0("Zoomed in on metabolite", + ifelse(n.obs > 2, "s", "")), + xlab = ifelse(ftmp$ds$time_unit == "", "Time", + paste("Time in", ftmp$ds$time_unit)), + ylab = ifelse(ds[[ds.i]]$unit == "", "Observed", + paste("Observed in", ftmp$ds$unit)), + ylim = c(0, max(subset(ftmp$data, + variable != parent)$observed))) + for (met in obs.vars[-1]) { + mkinresplot(ftmp, met, legend = FALSE, + main = paste("Residual plot for", met)) + } + } else { + mkinresplot(ftmp, parent, legend = FALSE, + main = paste("Residual plot for", parent), + xlab = ifelse(ftmp$ds$time_unit == "", "Time", + paste("Time in", ftmp$ds$time_unit)), + ylab = ifelse(ds[[ds.i]]$unit == "", "Residuals", + paste("Residuals in", ftmp$ds$unit))) + } + } + + tf2 <- get_tempfile(ext = ".png") + png(tf2, width = imgwidth / 50 , height = imgheight / 50, + units = "cm", res = 300, pointsize = ps) + make_plots() + dev.off() + + ghtml(paste0(""), + cont = pwg) +} +# vim: set foldmethod=marker ts=2 sw=2 expandtab: {{{1 -- cgit v1.2.1