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#' @title %<+%
#' @description
#' This operator attaches annotation data to a ggtree or ggsc graphic object
#' @rdname attacher
#' @param p ggplot2 object, such as ggtree or ggsc graphic object.
#' @param data data.frame, which must contains a column of \code{node},
#' or the first column of taxa labels, when \code{p} is a \code{ggtree} object.
#' Or it must contains columns of \code{.BarcodeID}, when \code{p} is a \code{ggsc}
#' object and \code{p$data} does not contain a column of \code{features}, if it
#' contains, the \code{data} must also contains a column of \code{features}.
#' @return ggplot object with annotation data added
#' @export
`%<+%` <- function(p, data){
if (! is.data.frame(data)) {
cli::cli_abort("right object should be a data.frame...")
}
if (missing(data)){
cli::cli_abort(c(
"Cannot use {.code %<+%} with a single argument.",
"i" = "Did you accidentally put {.code %<+%} on a new line?"
))
}
UseMethod("%<+%")
}
#' @method %<+% ggtree
#' @export
"%<+%.ggtree" <- function(p, data){
p <- p %add% data
return(p)
}
#' @method %<+% ggflow
#' @export
"%<+%.ggflow" <- function(p, data){
p$data <- merge_1st_with_label(p$data, data)
return(p)
}
#' @method %<+% ggsc
#' @export
"%<+%.ggsc" <- function(p, data){
if (inherits(p, 'patchwork')){
p$patches$plots <- lapply(p$patches$plots, function(x){
p <- left_join(x, data)
return(p)}) |>
suppressMessages()
}
p <- left_join(p, data) |> suppressMessages()
return(p)
}
`%add%` <- function(p, data) {
p$data <- p$data %add2% data
return(p)
}
##' @importFrom dplyr rename
##' @importFrom dplyr left_join
`%add2%` <- function(d1, d2) {
if ("node" %in% colnames(d2)) {
cn <- colnames(d2)
ii <- which(cn %in% c("node", cn[!cn %in% colnames(d1)]))
d2 <- d2[, ii]
dd <- dplyr::left_join(d1, d2, by="node")
} else {
dd <- merge_1st_with_label(d1, d2)
}
dd <- dd[match(d1$node, dd$node), ,drop=FALSE]
return(dd)
}
merge_1st_with_label <- function(d1, d2) {
d2[,1] <- as.character(unlist(d2[,1])) ## `unlist` to work with tbl_df
d2 <- dplyr::rename(d2, label = 1) ## rename first column name to 'label'
dd <- dplyr::left_join(d1, d2, by="label")
return(dd)
}
#' @importFrom dplyr left_join
#' @method left_join ggsc
#' @importFrom cli cli_warn
#' @export
left_join.ggsc <- function(x, y, by = NULL, copy = FALSE, suffix=c("", ".y"), ...){
dat <- x$data
msg <- c("The {.arg suffix} requires a character vector containing 2 different elements,",
"The first element must be \"\", and the second element must not be \"\",",
"it was set {.code suffix=c(\"\", \".y\")} automatically.")
if (all(nchar(suffix)!=0)){
cli::cli_warn(msg)
suffix[1] = ""
}
if (all(nchar(suffix)==0)){
cli::cli_warn(msg)
suffix[2] = ".y"
}
if (nchar(suffix[1])!=0 && nchar(suffix[2])==0){
cli::cli_warn(msg)
suffix <- rev(suffix[seq_len(2)])
}
if ('features' %in% names(dat) && length(unique(dat$features))>1 && !'features' %in% names(y)){
cli::cli_abort(c("The `features` contains in the column of {.cls {class(x)[1]}}, but ",
"the {.cls {class(y)[1]}} does not have `features` column."), call = NULL)
}
da <- dplyr::left_join(dat, y, by = by, copy = copy, suffix = suffix, ...)
x$data <- da
return(x)
}
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