R/define_comp_layout.R
In guiastrennec/modelviz: Generation of QMD for NONMEM outputs
Defines functions
define_comp_layout
Documented in
define_comp_layout
#' Create compartment layout
#'
#' @description Combine information for each compartment's rank, label, size,
#' color and scaling into a \code{data.frame}.
#'
#' @param qmd_info a \code{qmd_info} object generated with \code{import_qmd_info} or
#' \code{skeleton_qmd_info}
#' @param scaling logical if \code{TRUE} compartment size and colors will be scaled.
#' If \code{FALSE} standard model diagram will be created
#' @param rank integer vertor assigning a rank to each compartment. Can be used
#' to obtain a specific layout. The ranks must be greater or equal to 1.
#' @param comp_scale_fun a function to be used for compartment size scaling
#' @param color_scaling can be 'iiv', 'rse', 'none' or 'pbpk'
#' @param color_cutoff numeric vector of length 2 setting the cutoff limits in color coding
#' for RSE (\%) or IIV (\%)
#' @param filled logical if \code{TRUE} compartment will be filled
#' If \code{FALSE} only the compartment edges will be drawn
#' @param alpha transparency factor
#' @param comp_color_manual manually set color for each compartment
#' @param unscaled_color color of the unscaled compartments
#' @param unscaled_shape shape of the unscaled compartments. Can be square, circle or diamond
#' @param scaled_shape shape of the scaled compartments. Can be square, circle or diamond
#' @param font font name of the compartment label
#' @param comp_fontsize font size expansion factor
#'
#' @details The default \code{scaling_fun} argument is set to be a surface area
#' of the compartment.
#'
#' @seealso \code{\link{define_arrow_layout}}, \code{\link{import_qmd_info}}, \code{\link{qmd}}
#' @return A \code{data.frame}
#' @examples
#' \dontrun{
#' qmd_info <- import_qmd_info(dir = '../models/pk/', runno = '001')
#' comp <- define_comp_layout(qmd_info)
#' }
#' @export
#'
define_comp_layout <- function(qmd_info = NULL,
scaling = TRUE,
rank = NULL,
comp_scale_fun = function(x) { sqrt(x) },
color_scaling = 'RSE',
color_cutoff = c(25, 50),
filled = TRUE,
alpha = 1,
comp_color_manual = NULL,
unscaled_color = NULL,
unscaled_shape = 'circle',
scaled_shape = 'square',
font = 'Avenir',
comp_fontsize = 1) {
# Create key variables ----------------------------------------------------
node <- qmd_info$parsed_comp
# Dynamic QMDs
if (toupper(color_scaling) == 'DQMD') {
scaling <- TRUE
dqmd <- TRUE
} else {
dqmd <- FALSE
}
# Check inputs ------------------------------------------------------------
if (is.null(qmd_info)) {
stop('Argument \"qmd_info\" required.')
}
if (is.null(node)) {
stop('Level \"parsed_comp\" required in \"qmd_info\".')
}
if (qmd_info$advan == 10) {
stop('ADVAN 10 is not currently supported by modelviz.')
}
if (!is.null(node) && !all(c('label', 'prm', 'output') %in% colnames(node))) {
stop('Incorrect format of \"parsed_comp\" in \"qmd_info\", columns \"label\", \"prm\" and \"output\" required.')
}
if (scaling == FALSE) { node$prm <- NA }
# Start node data creation ------------------------------------------------
## Set node ranking
if (!is.null(rank)) {
if (all(is.numeric(rank)) && length(rank) == nrow(node)) {
node$rank <- rank
} else {
msg(paste0('Argument \"rank\" must be a numeric vector of length ', nrow(node), '.'), TRUE)
node$rank <- 1:nrow(node)
}
} else if (qmd_info$advan == 11) {
node$rank <- c(1, 2, 2)
} else if (qmd_info$advan == 12) {
node$rank <- c(1, 2, 3, 3)
} else {
node$rank <- 1:nrow(node)
}
## Create output compartment
if (any(node$output)) {
out_comp <- node[node$output, ]
out_comp$prm <- NA
out_comp$label <- paste0('Out_', out_comp$label)
node <- rbind(node, out_comp)
}
## Create node data.frame template
node$id <- 1:nrow(node)
node <- node[, c('id', 'label', 'rank', 'prm')]
node[, c('value', 'rse', 'iiv')] <- NA
## Ensure all prm exist
if (all(is.na(node$prm))) {
msg('Warning: No parameter provided in \"qmd_info$parsed_comp$prm\".', ifelse(scaling, TRUE, FALSE))
scaling <- FALSE
} else if (!all(node$prm[!is.na(node$prm)] %in% colnames(qmd_info$theta))) {
msg('Warning: Wrong parameter label provided in \"qmd_info$parsed_comp$prm\".', TRUE)
scaling <- FALSE
}
# Assign parameter values -------------------------------------------------
if (scaling | toupper(color_scaling) == 'DQMD') {
### Add bioavailability scaling if possible
if (!dqmd && any(grepl('^F\\d$', colnames(qmd_info$theta)))) {
ba_prm <- qmd_info$theta[1, grep('^F\\d$', colnames(qmd_info$theta)), drop = FALSE]
ba_comp <- as.numeric(gsub('\\D', '', colnames(ba_prm)))
if (!all(is.na(node$prm[node$id %in% ba_comp])) | any(ba_prm > 1)) {
msg('Warning: Any of the F (e.g. F1) parameters were either not accessible or >1.', TRUE)
} else {
node$prm[node$id %in% ba_comp] <- paste0('F', node$id[node$id %in% ba_comp])
}
}
### Assign all prm, rse, iiv
node[!is.na(node$prm), c('value', 'rse')] <- t(qmd_info$theta[, node[!is.na(node$prm), 'prm']])
### iiv labels assumed to have properly been cleaned in parse_ext_file
if (length(intersect(colnames(qmd_info$omega), node$prm)) > 0) {
node$iiv[which(node$prm %in% colnames(qmd_info$omega))] <-
t(qmd_info$omega)[match(node$prm[which(node$prm %in% colnames(qmd_info$omega))],
colnames(qmd_info$omega)),1]
node$iiv[node$iiv == 0] <- NA
}
}
# Format nodes ------------------------------------------------------------
## Special variables
comp_scale <- ifelse(scaling, 0.2 , 1) # Reduce entire graph size due to issues with big arrows in graphviz
if (dqmd) { comp_scale <- 0.5 }
comp_fontsize <- comp_scale * comp_fontsize * 15.5 # Base size is 15.5
node$fixedsize <- TRUE # Forces nodes to respect defined size
## Scaling factor
if (scaling & !dqmd) {
node$scale[!is.na(node$value) & !grepl('^F\\d$', node$prm)] <- comp_scale_fun(node$value[!is.na(node$value) & !grepl('^F\\d$', node$prm)])
node$width <- ifelse(!is.na(node$scale), node$scale, 1)
} else {
node$scale <- NA
node$width <- 1
}
## Fonts
node$fontsize <- comp_fontsize * node$width
node$fontname <- font
## Resolution adjustment
node$width <- node$width * comp_scale
node$height <- node$width
## Colors
if (!is.numeric(color_cutoff) || length(color_cutoff) != 2) {
msg('Argument \"color_cutoff\" must be a numeric vector of length of 2, units are in %.', TRUE)
color_scaling <- 'NONE'
}
if (is.null(unscaled_color)) {
unscaled_color <- ifelse(filled, 'grey80', 'black')
}
if (!is.null(comp_color_manual) & !dqmd) {
if (nrow(node[!grepl('Out_', node$label),]) %% length(comp_color_manual) > 0) {
stop('Inapropriate \"comp_color_manual\" provided.')
}
node$color <- 'black'
node$color[!grepl('Out_', node$label)] <- hex_color(comp_color_manual, alpha)
} else if ( (scaling == FALSE & toupper(color_scaling) != 'DQMD') | toupper(color_scaling) %in% c('NONE', 'PBPK')) {
node$color <- hex_color(unscaled_color, alpha)
} else if ((toupper(color_scaling) == 'RSE' & all(is.na(node$rse))) |
(toupper(color_scaling) == 'IIV' & all(is.na(node$iiv)))) {
msg(paste('Warning: Not enough information available on', color_scaling, 'for color scaling.'), TRUE)
node$color <- hex_color(unscaled_color, alpha)
} else if (toupper(color_scaling) == 'RSE') {
node$color[is.na(node$rse)] <- hex_color(unscaled_color, alpha) # light grey
node$color[node$rse <= color_cutoff[1]] <- hex_color('#B2E680', alpha) # green
node$color[node$rse > color_cutoff[1] &
node$rse < color_cutoff[2]] <- hex_color('#FFA366', alpha) # orange
node$color[node$rse > color_cutoff[2]] <- hex_color('#FF8080', alpha) # red
} else if (toupper(color_scaling) == 'IIV') {
node$color[is.na(node$iiv)] <- hex_color(unscaled_color, alpha) # light grey
node$color[node$iiv <= color_cutoff[1]] <- hex_color('#93D4EA', alpha) # light blue
node$color[node$iiv > color_cutoff[1] &
node$iiv < color_cutoff[2]] <- hex_color('#519BB4', alpha) # blue
node$color[node$iiv > color_cutoff[2]] <- hex_color('#5471B0', alpha) # dark blue
} else if (dqmd) {
node$color <- hex_color(unscaled_color, alpha) # light grey # Need more code safety
node$scale <- 0
node$scale[!is.na(node$value)] <- comp_scale_fun(node$value[!is.na(node$value)])
}
## Shapes
node$shape <- scaled_shape
node$shape[is.na(node$value) | grepl('^F\\d$', node$prm)] <- unscaled_shape
## Style
if (filled | dqmd) {
node$style <- 'filled'
node$fillcolor <- node$color
node$fontcolor <- 'black'
} else {
node$style <- 'solid'
node$fontcolor <- node$color
}
## dQMD
if (dqmd) {
if (!is.null(comp_color_manual)) {
node$fillcolor[!is.na(node$value)] <- paste0(hex_color(comp_color_manual, alpha) , ';',
node$scale[!is.na(node$value)], ':',
hex_color('white', 1))
} else {
node$fillcolor[!is.na(node$value)] <- paste0(hex_color('#519BB4', alpha) , ';',
node$scale[!is.na(node$value)], ':',
hex_color('white', 1))
}
node$fillcolor[!is.na(node$value) & node$value == 0] <- hex_color('white', 1)
node$gradientangle <- 90
}
## Format invisible nodes
node$style[grepl('Out_', node$label)] <- 'invis'
node$width[grepl('Out_', node$label)] <- 0
node$heigth[grepl('Out_', node$label)] <- 0
node$width[grepl('Out_', node$label)] <- 0
node$shape[grepl('Out_', node$label)] <- 'point'
node$penwidth <- ifelse(node$style %in% c('filled', 'invis') & !dqmd, 0, ifelse(scaling, 1, 2))
## Bioavailability
if (any(grepl('^F\\d$', node$prm))) {
node$style[grepl('^F\\d$', node$prm)] <- ifelse(unscaled_shape %in% c('circle', 'oval', 'ellipse'),
'wedged', 'striped')
node$penwidth[grepl('^F\\d$', node$prm)] <- 1.5
if (filled == FALSE) {
node$fillcolor <- hex_color('white', 1)
node$fontcolor[grepl('^F\\d$', node$prm)] <- hex_color('black', 1)
}
node$fillcolor[grepl('^F\\d$', node$prm)] <-
paste0(node$color[grepl('^F\\d$', node$prm)], ';', node$value[grepl('^F\\d$', node$prm)], ':', hex_color('white', 1))
node$color[grepl('^F\\d$', node$prm)] <- hex_color(node$color[grepl('^F\\d$', node$prm)], 1)
}
## Tooltip
node$tooltip[is.na(node$value)] <- node$label[is.na(node$value)]
node$tooltip[!is.na(node$value)] <- paste0(node$prm[!is.na(node$value)],' = ', signif(node$value[!is.na(node$value)], 4))
if (!dqmd) {
node$tooltip[!is.na(node$iiv)] <- paste0(node$tooltip[!is.na(node$iiv)], ' (', signif(node$iiv[!is.na(node$iiv)], 3), '% IIV)')
node$tooltip[!is.na(node$rse)] <- paste0(node$tooltip[!is.na(node$rse)], ' [', signif(node$rse[!is.na(node$rse)], 3), '% RSE]')
}
return(node)
} # End define_comp_layout
guiastrennec/modelviz documentation built on Feb. 16, 2024, 8:14 p.m.
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Defines functions define_comp_layout
Documented in define_comp_layout
#' Create compartment layout
#'
#' @description Combine information for each compartment's rank, label, size,
#' color and scaling into a \code{data.frame}.
#'
#' @param qmd_info a \code{qmd_info} object generated with \code{import_qmd_info} or
#' \code{skeleton_qmd_info}
#' @param scaling logical if \code{TRUE} compartment size and colors will be scaled.
#' If \code{FALSE} standard model diagram will be created
#' @param rank integer vertor assigning a rank to each compartment. Can be used
#' to obtain a specific layout. The ranks must be greater or equal to 1.
#' @param comp_scale_fun a function to be used for compartment size scaling
#' @param color_scaling can be 'iiv', 'rse', 'none' or 'pbpk'
#' @param color_cutoff numeric vector of length 2 setting the cutoff limits in color coding
#' for RSE (\%) or IIV (\%)
#' @param filled logical if \code{TRUE} compartment will be filled
#' If \code{FALSE} only the compartment edges will be drawn
#' @param alpha transparency factor
#' @param comp_color_manual manually set color for each compartment
#' @param unscaled_color color of the unscaled compartments
#' @param unscaled_shape shape of the unscaled compartments. Can be square, circle or diamond
#' @param scaled_shape shape of the scaled compartments. Can be square, circle or diamond
#' @param font font name of the compartment label
#' @param comp_fontsize font size expansion factor
#'
#' @details The default \code{scaling_fun} argument is set to be a surface area
#' of the compartment.
#'
#' @seealso \code{\link{define_arrow_layout}}, \code{\link{import_qmd_info}}, \code{\link{qmd}}
#' @return A \code{data.frame}
#' @examples
#' \dontrun{
#' qmd_info <- import_qmd_info(dir = '../models/pk/', runno = '001')
#' comp <- define_comp_layout(qmd_info)
#' }
#' @export
#'
define_comp_layout <- function(qmd_info = NULL,
scaling = TRUE,
rank = NULL,
comp_scale_fun = function(x) { sqrt(x) },
color_scaling = 'RSE',
color_cutoff = c(25, 50),
filled = TRUE,
alpha = 1,
comp_color_manual = NULL,
unscaled_color = NULL,
unscaled_shape = 'circle',
scaled_shape = 'square',
font = 'Avenir',
comp_fontsize = 1) {
# Create key variables ----------------------------------------------------
node <- qmd_info$parsed_comp
# Dynamic QMDs
if (toupper(color_scaling) == 'DQMD') {
scaling <- TRUE
dqmd <- TRUE
} else {
dqmd <- FALSE
}
# Check inputs ------------------------------------------------------------
if (is.null(qmd_info)) {
stop('Argument \"qmd_info\" required.')
}
if (is.null(node)) {
stop('Level \"parsed_comp\" required in \"qmd_info\".')
}
if (qmd_info$advan == 10) {
stop('ADVAN 10 is not currently supported by modelviz.')
}
if (!is.null(node) && !all(c('label', 'prm', 'output') %in% colnames(node))) {
stop('Incorrect format of \"parsed_comp\" in \"qmd_info\", columns \"label\", \"prm\" and \"output\" required.')
}
if (scaling == FALSE) { node$prm <- NA }
# Start node data creation ------------------------------------------------
## Set node ranking
if (!is.null(rank)) {
if (all(is.numeric(rank)) && length(rank) == nrow(node)) {
node$rank <- rank
} else {
msg(paste0('Argument \"rank\" must be a numeric vector of length ', nrow(node), '.'), TRUE)
node$rank <- 1:nrow(node)
}
} else if (qmd_info$advan == 11) {
node$rank <- c(1, 2, 2)
} else if (qmd_info$advan == 12) {
node$rank <- c(1, 2, 3, 3)
} else {
node$rank <- 1:nrow(node)
}
## Create output compartment
if (any(node$output)) {
out_comp <- node[node$output, ]
out_comp$prm <- NA
out_comp$label <- paste0('Out_', out_comp$label)
node <- rbind(node, out_comp)
}
## Create node data.frame template
node$id <- 1:nrow(node)
node <- node[, c('id', 'label', 'rank', 'prm')]
node[, c('value', 'rse', 'iiv')] <- NA
## Ensure all prm exist
if (all(is.na(node$prm))) {
msg('Warning: No parameter provided in \"qmd_info$parsed_comp$prm\".', ifelse(scaling, TRUE, FALSE))
scaling <- FALSE
} else if (!all(node$prm[!is.na(node$prm)] %in% colnames(qmd_info$theta))) {
msg('Warning: Wrong parameter label provided in \"qmd_info$parsed_comp$prm\".', TRUE)
scaling <- FALSE
}
# Assign parameter values -------------------------------------------------
if (scaling | toupper(color_scaling) == 'DQMD') {
### Add bioavailability scaling if possible
if (!dqmd && any(grepl('^F\\d$', colnames(qmd_info$theta)))) {
ba_prm <- qmd_info$theta[1, grep('^F\\d$', colnames(qmd_info$theta)), drop = FALSE]
ba_comp <- as.numeric(gsub('\\D', '', colnames(ba_prm)))
if (!all(is.na(node$prm[node$id %in% ba_comp])) | any(ba_prm > 1)) {
msg('Warning: Any of the F (e.g. F1) parameters were either not accessible or >1.', TRUE)
} else {
node$prm[node$id %in% ba_comp] <- paste0('F', node$id[node$id %in% ba_comp])
}
}
### Assign all prm, rse, iiv
node[!is.na(node$prm), c('value', 'rse')] <- t(qmd_info$theta[, node[!is.na(node$prm), 'prm']])
### iiv labels assumed to have properly been cleaned in parse_ext_file
if (length(intersect(colnames(qmd_info$omega), node$prm)) > 0) {
node$iiv[which(node$prm %in% colnames(qmd_info$omega))] <-
t(qmd_info$omega)[match(node$prm[which(node$prm %in% colnames(qmd_info$omega))],
colnames(qmd_info$omega)),1]
node$iiv[node$iiv == 0] <- NA
}
}
# Format nodes ------------------------------------------------------------
## Special variables
comp_scale <- ifelse(scaling, 0.2 , 1) # Reduce entire graph size due to issues with big arrows in graphviz
if (dqmd) { comp_scale <- 0.5 }
comp_fontsize <- comp_scale * comp_fontsize * 15.5 # Base size is 15.5
node$fixedsize <- TRUE # Forces nodes to respect defined size
## Scaling factor
if (scaling & !dqmd) {
node$scale[!is.na(node$value) & !grepl('^F\\d$', node$prm)] <- comp_scale_fun(node$value[!is.na(node$value) & !grepl('^F\\d$', node$prm)])
node$width <- ifelse(!is.na(node$scale), node$scale, 1)
} else {
node$scale <- NA
node$width <- 1
}
## Fonts
node$fontsize <- comp_fontsize * node$width
node$fontname <- font
## Resolution adjustment
node$width <- node$width * comp_scale
node$height <- node$width
## Colors
if (!is.numeric(color_cutoff) || length(color_cutoff) != 2) {
msg('Argument \"color_cutoff\" must be a numeric vector of length of 2, units are in %.', TRUE)
color_scaling <- 'NONE'
}
if (is.null(unscaled_color)) {
unscaled_color <- ifelse(filled, 'grey80', 'black')
}
if (!is.null(comp_color_manual) & !dqmd) {
if (nrow(node[!grepl('Out_', node$label),]) %% length(comp_color_manual) > 0) {
stop('Inapropriate \"comp_color_manual\" provided.')
}
node$color <- 'black'
node$color[!grepl('Out_', node$label)] <- hex_color(comp_color_manual, alpha)
} else if ( (scaling == FALSE & toupper(color_scaling) != 'DQMD') | toupper(color_scaling) %in% c('NONE', 'PBPK')) {
node$color <- hex_color(unscaled_color, alpha)
} else if ((toupper(color_scaling) == 'RSE' & all(is.na(node$rse))) |
(toupper(color_scaling) == 'IIV' & all(is.na(node$iiv)))) {
msg(paste('Warning: Not enough information available on', color_scaling, 'for color scaling.'), TRUE)
node$color <- hex_color(unscaled_color, alpha)
} else if (toupper(color_scaling) == 'RSE') {
node$color[is.na(node$rse)] <- hex_color(unscaled_color, alpha) # light grey
node$color[node$rse <= color_cutoff[1]] <- hex_color('#B2E680', alpha) # green
node$color[node$rse > color_cutoff[1] &
node$rse < color_cutoff[2]] <- hex_color('#FFA366', alpha) # orange
node$color[node$rse > color_cutoff[2]] <- hex_color('#FF8080', alpha) # red
} else if (toupper(color_scaling) == 'IIV') {
node$color[is.na(node$iiv)] <- hex_color(unscaled_color, alpha) # light grey
node$color[node$iiv <= color_cutoff[1]] <- hex_color('#93D4EA', alpha) # light blue
node$color[node$iiv > color_cutoff[1] &
node$iiv < color_cutoff[2]] <- hex_color('#519BB4', alpha) # blue
node$color[node$iiv > color_cutoff[2]] <- hex_color('#5471B0', alpha) # dark blue
} else if (dqmd) {
node$color <- hex_color(unscaled_color, alpha) # light grey # Need more code safety
node$scale <- 0
node$scale[!is.na(node$value)] <- comp_scale_fun(node$value[!is.na(node$value)])
}
## Shapes
node$shape <- scaled_shape
node$shape[is.na(node$value) | grepl('^F\\d$', node$prm)] <- unscaled_shape
## Style
if (filled | dqmd) {
node$style <- 'filled'
node$fillcolor <- node$color
node$fontcolor <- 'black'
} else {
node$style <- 'solid'
node$fontcolor <- node$color
}
## dQMD
if (dqmd) {
if (!is.null(comp_color_manual)) {
node$fillcolor[!is.na(node$value)] <- paste0(hex_color(comp_color_manual, alpha) , ';',
node$scale[!is.na(node$value)], ':',
hex_color('white', 1))
} else {
node$fillcolor[!is.na(node$value)] <- paste0(hex_color('#519BB4', alpha) , ';',
node$scale[!is.na(node$value)], ':',
hex_color('white', 1))
}
node$fillcolor[!is.na(node$value) & node$value == 0] <- hex_color('white', 1)
node$gradientangle <- 90
}
## Format invisible nodes
node$style[grepl('Out_', node$label)] <- 'invis'
node$width[grepl('Out_', node$label)] <- 0
node$heigth[grepl('Out_', node$label)] <- 0
node$width[grepl('Out_', node$label)] <- 0
node$shape[grepl('Out_', node$label)] <- 'point'
node$penwidth <- ifelse(node$style %in% c('filled', 'invis') & !dqmd, 0, ifelse(scaling, 1, 2))
## Bioavailability
if (any(grepl('^F\\d$', node$prm))) {
node$style[grepl('^F\\d$', node$prm)] <- ifelse(unscaled_shape %in% c('circle', 'oval', 'ellipse'),
'wedged', 'striped')
node$penwidth[grepl('^F\\d$', node$prm)] <- 1.5
if (filled == FALSE) {
node$fillcolor <- hex_color('white', 1)
node$fontcolor[grepl('^F\\d$', node$prm)] <- hex_color('black', 1)
}
node$fillcolor[grepl('^F\\d$', node$prm)] <-
paste0(node$color[grepl('^F\\d$', node$prm)], ';', node$value[grepl('^F\\d$', node$prm)], ':', hex_color('white', 1))
node$color[grepl('^F\\d$', node$prm)] <- hex_color(node$color[grepl('^F\\d$', node$prm)], 1)
}
## Tooltip
node$tooltip[is.na(node$value)] <- node$label[is.na(node$value)]
node$tooltip[!is.na(node$value)] <- paste0(node$prm[!is.na(node$value)],' = ', signif(node$value[!is.na(node$value)], 4))
if (!dqmd) {
node$tooltip[!is.na(node$iiv)] <- paste0(node$tooltip[!is.na(node$iiv)], ' (', signif(node$iiv[!is.na(node$iiv)], 3), '% IIV)')
node$tooltip[!is.na(node$rse)] <- paste0(node$tooltip[!is.na(node$rse)], ' [', signif(node$rse[!is.na(node$rse)], 3), '% RSE]')
}
return(node)
} # End define_comp_layout
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