Nothing
#' Get title for \code{view_xifti_surface} or \code{view_xifti_volume}
#'
#' Determine the title(s) for the cortical surface or subcortical volume plot,
#' if it was not provided by the user.
#'
#' @param xifti_meta \code{xifti$meta}
#' @param idx The index
#'
#' @return The RGL object ID for the title
#'
#' @keywords internal
#'
view_xifti.title <- function(xifti_meta, idx){
intent <- xifti_meta$cifti$intent
if (is.null(intent)) {
if (!is.null(xifti_meta$cifti$names) && length(xifti_meta$cifti$names)>=idx) {
title <- xifti_meta$cifti$names[idx]
} else {
title <- ""
}
} else if (intent == 3002) {
title <- paste("Index", idx)
if (!any(vapply(xifti_meta$cifti[c("time_start", "time_step", "time_unit")], is.null, FALSE))) {
title <- paste0(
title, " (",
xifti_meta$cifti$time_start+xifti_meta$cifti$time_step*idx,
" ", xifti_meta$cifti$time_unit, "s)"
)
}
} else if (intent == 3006) {
if (!is.null(xifti_meta$cifti$names) && length(xifti_meta$cifti$names)>=idx) {
title <- xifti_meta$cifti$names[idx]
} else {
title <- ""
}
} else if (intent == 3007) {
if (!is.null(xifti_meta$cifti$labels) && length(xifti_meta$cifti$labels)>=idx) {
title <- names(xifti_meta$cifti$labels)[idx]
} else {
title <- ""
}
}
title
}
#' Make the colorbar for \code{view_xifti_surface}
#'
#' See \code{\link{view_xifti_surface}} for details.
#'
#' @param pal_base Base palette
#' @param pal Full palette
#' @param color_mode See \code{\link{view_xifti_surface}}
#' @param text_color Color of text
#' @param digits See \code{\link{view_xifti_surface}}
#'
#' @return A list of keyword arguments to \code{\link[fields]{image.plot}}
#'
#' @keywords internal
#'
view_xifti.cbar <- function(pal_base, pal, color_mode, text_color, digits, scientific=NA) {
colorbar_breaks <- c(
pal_base$value[1],
pal$value[1:(length(pal$value)-1)] + diff(pal$value)/2,
pal$value[length(pal$value)]
)
colorbar_breaks <- unique(colorbar_breaks)
colorbar_labs <- switch(color_mode,
sequential=c(
pal_base$value[1],
pal_base$value[nrow(pal_base)]
),
qualitative=seq_len(nrow(pal_base)),
diverging=c(
pal_base$value[1],
pal_base$value[as.integer(ceiling(nrow(pal_base)/2))],
pal_base$value[nrow(pal_base)]
)
)
if (length(colorbar_breaks) == 1) {
colorbar_kwargs <- list(
legend.only=TRUE,
zlim=c(1,2),
col=rep(pal$color[1], 2),
breaks=c(0, 1, 2),
axis.args=list(at=1, labels=colorbar_breaks)
)
} else {
colorbar_kwargs <- list(
legend.only = TRUE,
zlim = range(pal$value),
col = as.character(pal$color),
breaks=colorbar_breaks,
#legend.lab=colorbar_label,
axis.args=list(
cex.axis=1.7, # size of labels (numeric limits)
at=colorbar_labs,
col=text_color, col.ticks=text_color, col.axis=text_color,
labels=format(colorbar_labs, digits=digits, scientific=scientific)
)
)
}
colorbar_kwargs <- c(colorbar_kwargs,
list(
horizontal=TRUE, # horizontal legend
legend.cex=2, # not sure what this does?
#legend.shrink=.5, # half the width of the legend #override by smallplot
#legend.width=1.67, # height of colorbar #override by smallplot
legend.line=5, # height of lines between labels and colorbar
#legend.mar=4, # legend margin #override by smallplot
smallplot=c(.15, .5, .65, 1) # x1 x2 y1 y2
)
)
}
#' Draw color legend for qualitative mode
#'
#' See \code{\link{view_xifti_surface}} for details.
#'
#' @param pal_base Base palette + labels for each row
#' @param leg_ncol Number of columns in legend.
#' @param text_color Color of text
#' @param scale of text
#'
#' @return A color legend from ggplot2
#'
#' @keywords internal
#'
view_xifti.cleg <- function(pal_base, leg_ncol, text_color, scale=1, title_sub=FALSE){
if (!requireNamespace("ggplot2", quietly = TRUE)) {
stop("Package \"ggplot2\" needed to make the color legend. Please install it.", call. = FALSE)
}
if (!requireNamespace("ggpubr", quietly = TRUE)) {
stop("Package \"ggpubr\" needed to make the color legend. Please install it.", call. = FALSE)
}
point_size <- 5 * scale
legend_title_size <- 1.5 * scale
legend_text_size <- 1.2 * scale
if (is.null(leg_ncol)) { leg_ncol <- floor(sqrt(nrow(pal_base))) }
colors2 <- pal_base$color; names(colors2) <- pal_base$labels
value <- NULL
plt <- ggplot2::ggplot(data=pal_base, ggplot2::aes(x=value, y=value, fill=labels)) +
ggplot2::geom_point(size=point_size, shape=22, color="black") + ggplot2::theme_bw() +
ggplot2::scale_fill_manual(values=colors2, name=ifelse(title_sub, "Labels (subcortex)", "Labels")) +
ggplot2::guides(fill=ggplot2::guide_legend(label.theme=ggplot2::element_text(color=text_color), ncol=leg_ncol)) +
ggplot2::theme(legend.title=ggplot2::element_text(
size=ggplot2::rel(legend_title_size)),
legend.text=ggplot2::element_text(color=text_color, size=ggplot2::rel(legend_text_size))
)
leg <- ggpubr::as_ggplot(ggpubr::get_legend(plt))
}
#' View a \code{"xifti"} object
#'
#' Displays the data in a \code{"xifti"} object using \code{\link{view_xifti_surface}}
#' and/or \code{\link{view_xifti_volume}}. Compared to calling these two
#' functions separately on the same data, this function may be more convenient
#' since the automatic choice of color mode and limits is determined across
#' the entire data and shared between the two plots. Also, if writing files
#' the subcortical plots will not overwrite the cortical plots.
#'
#' @inheritParams xifti_Param
#' @param what \code{"surface"}, \code{"volume"}, or \code{"both"}. \code{NULL}
#' will infer based on the contents of the \code{"xifti"}: if there is data,
#' plot the surface cortex data if present, and the volumetric subcortical data
#' otherwise. If there is no data, plot the surface geometry if present, and
#' do nothing otherwise.
#' @param ... Additional arguments to pass to either view function.
#'
#' @return The return value of \code{view_xifti_surface} or
#' \code{view_xifti_volume}.
#'
#' @family common
#' @family visualizing
#' @export
#'
view_xifti <- function(xifti, what=NULL, ...) {
stopifnot(is.xifti(xifti))
has_left <- !is.null(xifti$data$cortex_left)
has_right <- !is.null(xifti$data$cortex_right)
has_sub <- !is.null(xifti$data$subcort)
has_surfL <- !is.null(xifti$surf$cortex_left)
has_surfR <- !is.null(xifti$surf$cortex_right)
out <- list(surface = NULL, volume = NULL)
if (is.null(what)) {
if ((has_left | has_right) & has_sub) {
what <- "both"
} else if (has_left | has_right) {
what <- "surface"
} else if (has_sub) {
what <- "volume"
} else if (has_surfL | has_surfR) {
what <- "surface"
} else {
cat("Nothing to plot: the `xifti` is empty.\n")
return(NULL)
}
} else {
what <- match.arg(what, c("surface", "volume", "both"))
if (what == "both" || what == "surface") {
if (!any(c(has_left, has_right, has_surfL, has_surfR))) {
stop("No cortical data nor surface geometry are present in the `xifti`, so the surface cannot be plotted.")
}
}
if (what == "both" || what == "volume") {
if (!has_sub) {
stop("No subcortical data are present in the `xifti`, so the volume cannnot be plotted.")
}
}
}
args <- list(...)
vxs <- function(
xifti, args, color_mode, zlim, colors,
fname, fname_sub,
structural_img, plane, convention, n_slices, slices,
ypos.title, xpos.title, orientation_labels,
...
) {
view_xifti_surface(
xifti, color_mode=args$color_mode, zlim=args$zlim, colors=args$colors,
fname=args[["fname"]], ...
)
}
vxv <- function(
xifti, args, color_mode, zlim, colors,
fname, fname_sub,
legend_fname,
surfL, surfR, hemisphere, view, slider_title, borders, alpha,
edge_color, vertex_color, vertex_size, material, zoom,
...
) {
view_xifti_volume(
xifti, color_mode=args$color_mode, zlim=args$zlim, colors=args$colors,
fname=args[["fname"]], fname_sub=args[["fname_sub"]],
legend_fname=args$legend_fname,
...
)
}
if (length(args$widget) > 1) {
args$widget <- as.logical(args$widget[[1]])
}
# If `both`, show cortex only if making a widget, and do not write out overlapping
# file names. ----------------------------------------------------------------
args[["fname_sub"]] <- FALSE
if (what == "both") {
if (isTRUE(args$widget)) {
warning(
"Only one widget can be made at a time. ",
"Plotting the cortex only. ",
"Use a separate command to display the subcortex.\n"
)
args$widget <- TRUE
what <- "surface"
} else if (length(args$idx) > 1 && (isFALSE(args[["fname"]]) || is.null(args[["fname"]]))) {
warning(
"A widget is needed to display more than one column for the cortex. ",
"But, only one widget can be made at a time. ",
"Plotting the cortex only. ",
"Use a separate command to display the subcortex.\n"
)
args$widget <- TRUE
what <- "surface"
}
args[["fname_sub"]] <- TRUE
} else if (what == "surface") {
if (length(args$idx) > 1 && (isFALSE(args[["fname"]]) || is.null(args[["fname"]]))) {
args$widget <- TRUE
}
}
# If `both`, use the same zlim, colors, and color_mode -----------------------
made_same <- FALSE
if (what == "both") {
if (is.null(args$idx)) { args$idx <- 1 }
args$idx <- as.numeric(args$idx)
stopifnot(all(args$idx > 0) && all(args$idx <= ncol(xifti)))
if (is.null(args$color_mode)) { args$color_mode <- "auto" }
if (args$color_mode == "auto") {
if (!is.null(xifti$meta$cifti$intent) && xifti$meta$cifti$intent==3007) {
args$color_mode <- "qualitative"
}
# Otherwise, set after call to view_xifti_surface.mesh_val
} else {
args$color_mode <- match.arg(args$color_mode, c("sequential", "qualitative", "diverging"))
}
values <- as.vector(as.matrix(xifti)[,args$idx])
if (!is.null(values)) {
# Determine `color_mode` and `colors`
if (args$color_mode == "sequential")
if (args$color_mode == "auto" || is.null(args$colors)) {
if (args$color_mode == "auto") {
if (length(args$zlim) == 3) {
args$color_mode <- "diverging"
} else if (is.null(values) || all(values %in% c(NA, NaN))) {
args$color_mode <- "diverging"
if (is.null(args$colors)) { args$colors <- "ROY_BIG_BL" }
} else if (length(args$zlim) == 2) {
args$color_mode <- ifelse(prod(args$zlim) >= 0, "sequential", "diverging")
}
}
if (args$color_mode == "auto" || (args$color_mode!="qualitative" && is.null(args$colors))) {
pctile_05 <- quantile(values, .05, na.rm=TRUE)
pctile_95 <- quantile(values, .95, na.rm=TRUE)
pctile_05_neg <- pctile_05 < 0
pctile_95_pos <- pctile_95 > 0
if (args$color_mode == "sequential") {
args$colors <- ifelse(pctile_05_neg, "ROY_BIG_BL_neg", "ROY_BIG_BL_pos")
}
if (!xor(pctile_05_neg, pctile_95_pos)) {
if (args$color_mode == "auto") { args$color_mode <- "diverging" }
if (is.null(args$colors)) { args$colors <- "ROY_BIG_BL" }
} else if (pctile_95_pos) {
if (args$color_mode == "auto") { args$color_mode <- "sequential" }
if (is.null(args$colors)) { args$colors <- "ROY_BIG_BL_pos" }
} else if (pctile_05_neg) {
if (args$color_mode == "auto") { args$color_mode <- "sequential" }
if (is.null(args$colors)) { args$colors <- "ROY_BIG_BL_neg" }
} else { stop() }
}
}
# Determine `zlim`
if (!args$color_mode=="qualitative") {
# Use same iff not qualitative and some colors -------------------------
made_same <- TRUE
if (is.null(args$zlim)) {
if (is.null(args$digits)) {
signif_digits <- 3
} else {
signif_digits <- args$digits
}
DATA_MIN <- signif(min(values, na.rm=TRUE), signif_digits)
DATA_MAX <- signif(max(values, na.rm=TRUE), signif_digits)
pctile_05 <- signif(quantile(values, .05, na.rm=TRUE), signif_digits)
pctile_95 <- signif(quantile(values, .95, na.rm=TRUE), signif_digits)
pctile_05_neg <- pctile_05 < 0
pctile_95_pos <- pctile_95 > 0
if (!pctile_05_neg) {
if (pctile_95 == 0) { pctile_95 <- DATA_MAX }
args$zlim <- c(0, pctile_95)
} else if (!pctile_95_pos) {
if (pctile_05 == 0) { pctile_05 <- DATA_MAX }
args$zlim <- c(pctile_05, 0)
} else {
pctile_max <- max(abs(c(pctile_05, pctile_95)))
if (pctile_max == 0) { pctile_max <- max(abs(c(DATA_MIN, DATA_MAX))) }
if (args$color_mode=="diverging") {
args$zlim <- c(-pctile_max, 0, pctile_max)
} else {
args$zlim <- c(-pctile_max, pctile_max)
}
}
message(
"`zlim` not provided: using color range ",
as.character(min(args$zlim)), " - ", as.character(max(args$zlim)), " ",
"(data limits: ", as.character(min(DATA_MIN)), " - ",
as.character(max(DATA_MAX)), ")."
)
}
}
}
}
# ----------------------------------------------------------------------------
if (what == "both" | what == "surface") {
out$surface <- vxs(xifti, args, ...)
}
if (what == "both" | what == "volume") {
args2 <- args
write_dummy_legend <- what == "both" && args2$color_mode != "qualitative" && "legend_embed" %in% names(args2) && args2$legend_embed==FALSE
if (write_dummy_legend) {
dummy_legend_fname <- tempfile(fileext=".png")
args2$legend_fname <- dummy_legend_fname
} else if (!("legend_fname" %in% names(args2))) {
args2$legend_fname <- "[fname]_legend"
}
out$volume <- vxv(xifti, args2, ...)
if (write_dummy_legend) {
out$volume <- out$volume[!(out$volume == dummy_legend_fname)]
}
}
out <- switch(what,
both = out,
surface = out$surface,
volume = out$volume
)
if (isTRUE(args$widget)) {
return(out)
} else {
return(invisible(out))
}
}
#' S3 method: use \code{view_xifti} to plot a \code{"xifti"} object
#'
#' @inheritParams x_Param_xifti
#' @param ... Additional arguments to \code{\link{view_xifti}}, except
#' \code{what}, which will be set to \code{NULL}.
#'
#' @method plot xifti
#'
#' @export
#'
plot.xifti <- function(x, ...){
view_xifti(x, ...)
}
#' @rdname view_xifti
#' @export
view_cifti <- function(xifti, ...){
view_xifti(xifti, ...)
}
#' @rdname view_xifti
#' @export
viewCIfTI <- function(xifti, ...){
view_xifti(xifti, ...)
}
#' @rdname view_xifti
#' @export
viewcii <- function(xifti, ...){
view_xifti(xifti, ...)
}
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