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#' Track code for the plots
#'
#' Fetches all the code that was used to generate the plots during the live iSEE session.
#'
#' @param pObjects An environment containing global parameters generated in the \code{\link{iSEE}} app.
#' @param all_memory A list of \linkS4class{Panel}s representing the current state of the application.
#' @param graph A \link{graph} object containing point selection links between panels.
#' @param commands A list of lists of character vectors, where each internal list contains commands to generate each panel.
#' @param varname A list of strings containing the variable name for the contents of each panel.
#' @param se_name String containing the initial name of the SummarizedExperiment or SingleCellExperiment object.
#' @param ecm_name String containing the initial name of the ExperimentColorMap in use.
#' @param mod_commands Character vector of commands to modify the SummarizedExperiment or ExperimentColorMap at the start.
#'
#' @return A character vector containing all lines of code (plus comments), to use in the \code{shinyAce} editor in \code{\link{iSEE}}.
#'
#' @author Federico Marini
#' @rdname INTERNAL_track_it_all
.track_it_all <- function(pObjects, se_name, ecm_name, mod_commands=character(0)) {
tracked_code <- c(
"## The following list of commands will generate the plots created in iSEE",
"## Copy them into a script or an R session containing your SingleCellExperiment.",
"## All commands below refer to your SingleCellExperiment object as `se`.",
"",
sprintf("se <- %s", se_name),
sprintf("colormap <- %s", ecm_name),
mod_commands,
sprintf("colormap <- synchronizeAssays(colormap, se)"),
"all_contents <- list()",
"",
.track_selection_code(pObjects$memory),
.track_plotting_code(pObjects$memory, pObjects$selection_links, pObjects$commands, pObjects$varname),
strrep("#", 80),
"## To guarantee the reproducibility of your code, you should also",
"## record the output of sessionInfo()",
"sessionInfo()")
# Restoring indenting for multi-line ggplot code.
ggplot_ix <- grep("\\+$", tracked_code) + 1L
to_mod <- tracked_code[ggplot_ix]
to_mod <- paste0(" ", to_mod)
to_mod <- gsub("\n", "\n ", to_mod)
tracked_code[ggplot_ix] <- to_mod
return(tracked_code)
}
#' @describeIn INTERNAL_track_it_all Returns a character vector of commands that create brushes, lassos, and selection history.
.track_selection_code <- function(all_memory) {
brush_code <- history_code <- list()
for (panel_name in names(all_memory)) {
instance <- all_memory[[panel_name]]
if (!is(instance, "DotPlot")) {
next
}
brush_struct <- all_memory[[panel_name]][[.brushData]]
if (!is.null(brush_struct)) {
brush_struct <- .deparse_for_viewing(brush_struct)
brush_code[[panel_name]] <- sprintf("all_active[['%s']] <- %s", panel_name, brush_struct)
}
saved_struct <- all_memory[[panel_name]][[.multiSelectHistory]]
if (length(saved_struct)) {
saved_struct <- .deparse_for_viewing(saved_struct)
history_code[[panel_name]] <- sprintf("all_saved[['%s']] <- %s", panel_name, saved_struct)
}
}
tracked_code <- list(character(0), character(0))
if (any(lengths(brush_code) > 0)) {
tracked_code[[1]] <- c(strrep("#", 80),
"# Defining brushes",
strrep("#", 80), "",
"all_active <- list()",
unlist(brush_code), "")
}
if (any(lengths(history_code) > 0)) {
tracked_code[[2]] <- c(strrep("#", 80),
"# Defining selection histories",
strrep("#", 80), "",
"all_saved <- list()",
unlist(history_code), "")
}
unlist(tracked_code)
}
#' @rdname INTERNAL_track_it_all
#' @importFrom igraph topo_sort
.track_plotting_code <- function(all_memory, graph, commands, varname) {
all_tracks <- list()
ordering <- names(topo_sort(graph, "out"))
for (panel_name in ordering) {
instance <- all_memory[[panel_name]]
header_comments <- c(strrep("#", 80),
paste("##", .getFullName(instance)),
strrep("#", 80),
"")
# Adding the plotting commands.
collated <- character(0)
for (cmds in commands[[panel_name]]) {
collated <- c(collated, cmds, "")
}
# Saving data for transmission after selections have been processed;
# this is the equivalent point in .create_plots() where coordinates are saved.
var <- varname[[panel_name]]
if (!is.null(var)) {
collated <- c(collated, "# Saving data for transmission",
sprintf("all_contents[['%s']] <- %s", panel_name, var),
"")
}
all_tracks[[panel_name]] <- c(header_comments, collated)
}
unlist(all_tracks)
}
#' Deparse R expressions for viewing
#'
#' Generate the command required to produce an R object, in a multi-line string with appropriate indenting.
#'
#' @param exprs An R expression to be deparsed.
#' @param indent An integer scalar specifying the indent level.
#'
#' @return A string containing the R command to produce \code{exprs}.
#'
#' @author Aaron Lun
#' @rdname INTERNAL_deparse_for_viewing
#' @seealso
#' \code{\link{.track_it_all}}
#' \code{\link{.report_memory}}
.deparse_for_viewing <- function(exprs, indent=1) {
paste(deparse(exprs, width.cutoff=80),
collapse=paste0("\n", strrep(" ", indent*4)))
}
#' Plot a snapshot of the links among panels
#'
#' Creates a graph of the current links among all currently active panels, and plots it.
#'
#' @param graph A \link{graph} containing panels as nodes and directional edges as transmissions of multiple selections.
#' @param panel_colors A named character vector of colors for each panel.
#'
#' @return Plots the graph representing the snapshot of links among plots/panels
#' @author Federico Marini
#' @rdname INTERNAL_snapshot_graph_linkedpanels
#' @importFrom graphics plot
.snapshot_graph_linkedpanels <- function(graph, panel_colors) {
plot(graph,
edge.arrow.size = .8,
vertex.label.cex = 1.3,
vertex.label.family = "Helvetica",
vertex.label.color = "black",
vertex.label.dist = 2.5,
vertex.color = panel_colors[names(V(graph))])
}
#' Report current memory state
#'
#' Report the R commands necessary to reproduce the memory state of the interface.
#'
#' @param all_memory A list of \linkS4class{Panel} objects representing the current state of the application.
#'
#' @return A character vector of commands necessary to produce \code{all_memory}.
#'
#' @author Aaron Lun
#' @rdname INTERNAL_report_memory
#' @seealso
#' \code{\link{iSEE}}
.report_memory <- function(all_memory) {
collected <- list("initial <- list()")
for (i in names(all_memory)) {
panel <- all_memory[[i]]
collected[[i]] <- list(
"",
strrep("#", 80),
sprintf("# Settings for %s", .getFullName(panel)),
strrep("#", 80), "",
paste(
sprintf("initial[[%s]] <-", deparse(i)),
paste(deparse(panel), collapse="\n")
)
)
}
unlist(collected)
}
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