# PLOT SPOT
#' @include AllClasses.R AllGenerics.R
NULL
#' @export
#' @rdname plot_spot
#' @aliases plot_spot,matrix-method
setMethod(
f = "plot_spot",
signature = signature(object = "matrix"),
definition = function(object, type = c("ring", "plain"),
col = grDevices::hcl.colors(12, "YlOrBr", rev = TRUE),
diag = TRUE, upper = TRUE, lower = TRUE,
freq = FALSE, margin = 1,
axes = TRUE, legend = TRUE, ...) {
## Validation
type <- match.arg(type, several.ok = FALSE)
plot_matrix(object, panel = panel_spot, col = col,
diag = diag, upper = upper, lower = lower,
freq = freq, margin = margin, drop_zero = TRUE,
axes = axes, legend = legend, type = type)
invisible(object)
}
)
#' @export
#' @rdname plot_spot
#' @aliases plot_spot,data.frame-method
setMethod(
f = "plot_spot",
signature = signature(object = "data.frame"),
definition = function(object, type = c("ring", "plain"),
col = grDevices::hcl.colors(12, "YlOrBr", rev = TRUE),
diag = TRUE, upper = TRUE, lower = TRUE,
freq = FALSE, margin = 1,
axes = TRUE, legend = TRUE, ...) {
object <- data.matrix(object)
methods::callGeneric(object, type = type, col = col,
diag = diag, upper = upper, lower = lower,
freq = freq, margin = margin,
axes = axes, legend = legend, ...)
}
)
#' @export
#' @rdname plot_spot
#' @aliases plot_spot,dist-method
setMethod(
f = "plot_spot",
signature = signature(object = "dist"),
definition = function(object, type = c("ring", "plain"),
col = grDevices::hcl.colors(12, "YlOrBr", rev = TRUE),
diag = FALSE, upper = FALSE, lower = !upper,
axes = TRUE, legend = TRUE, ...) {
# index_name <- attr(object, "method")
object <- as.matrix(object)
methods::callGeneric(object, type = type, col = col,
diag = diag, upper = upper, lower = lower,
axes = axes, legend = legend)
}
)
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