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/mkinGUI.R | 826 ----------------------------------------------------- 1 file changed, 826 deletions(-) delete mode 100644 inst/GUI/mkinGUI.R (limited to 'inst/GUI/mkinGUI.R') diff --git a/inst/GUI/mkinGUI.R b/inst/GUI/mkinGUI.R deleted file mode 100644 index 07f892e0..00000000 --- a/inst/GUI/mkinGUI.R +++ /dev/null @@ -1,826 +0,0 @@ -# $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