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# ggplot backend for the xgboost plotting facilities
#' @rdname xgb.plot.importance
#' @export
xgb.ggplot.importance <- function(importance_matrix = NULL, top_n = NULL, measure = NULL,
rel_to_first = FALSE, n_clusters = c(1:10), ...) {
importance_matrix <- xgb.plot.importance(importance_matrix, top_n = top_n, measure = measure,
rel_to_first = rel_to_first, plot = FALSE, ...)
if (!requireNamespace("ggplot2", quietly = TRUE)) {
stop("ggplot2 package is required", call. = FALSE)
}
if (!requireNamespace("Ckmeans.1d.dp", quietly = TRUE)) {
stop("Ckmeans.1d.dp package is required", call. = FALSE)
}
clusters <- suppressWarnings(
Ckmeans.1d.dp::Ckmeans.1d.dp(importance_matrix$Importance, n_clusters)
)
importance_matrix[, Cluster := as.character(clusters$cluster)]
plot <-
ggplot2::ggplot(importance_matrix,
ggplot2::aes(x = factor(Feature, levels = rev(Feature)), y = Importance, width = 0.5),
environment = environment()) +
ggplot2::geom_bar(ggplot2::aes(fill = Cluster), stat = "identity", position = "identity") +
ggplot2::coord_flip() +
ggplot2::xlab("Features") +
ggplot2::ggtitle("Feature importance") +
ggplot2::theme(plot.title = ggplot2::element_text(lineheight = .9, face = "bold"),
panel.grid.major.y = ggplot2::element_blank())
return(plot)
}
#' @rdname xgb.plot.deepness
#' @export
xgb.ggplot.deepness <- function(model = NULL, which = c("2x1", "max.depth", "med.depth", "med.weight")) {
if (!requireNamespace("ggplot2", quietly = TRUE))
stop("ggplot2 package is required for plotting the graph deepness.", call. = FALSE)
which <- match.arg(which)
dt_depths <- xgb.plot.deepness(model = model, plot = FALSE)
dt_summaries <- dt_depths[, .(.N, Cover = mean(Cover)), Depth]
setkey(dt_summaries, 'Depth')
if (which == "2x1") {
p1 <-
ggplot2::ggplot(dt_summaries) +
ggplot2::geom_bar(ggplot2::aes(x = Depth, y = N), stat = "Identity") +
ggplot2::xlab("") +
ggplot2::ylab("Number of leafs") +
ggplot2::ggtitle("Model complexity") +
ggplot2::theme(
plot.title = ggplot2::element_text(lineheight = 0.9, face = "bold"),
panel.grid.major.y = ggplot2::element_blank(),
axis.ticks = ggplot2::element_blank(),
axis.text.x = ggplot2::element_blank()
)
p2 <-
ggplot2::ggplot(dt_summaries) +
ggplot2::geom_bar(ggplot2::aes(x = Depth, y = Cover), stat = "Identity") +
ggplot2::xlab("Leaf depth") +
ggplot2::ylab("Weighted cover")
multiplot(p1, p2, cols = 1)
return(invisible(list(p1, p2)))
} else if (which == "max.depth") {
p <-
ggplot2::ggplot(dt_depths[, max(Depth), Tree]) +
ggplot2::geom_jitter(ggplot2::aes(x = Tree, y = V1),
height = 0.15, alpha = 0.4, size = 3, stroke = 0) +
ggplot2::xlab("tree #") +
ggplot2::ylab("Max tree leaf depth")
return(p)
} else if (which == "med.depth") {
p <-
ggplot2::ggplot(dt_depths[, median(as.numeric(Depth)), Tree]) +
ggplot2::geom_jitter(ggplot2::aes(x = Tree, y = V1),
height = 0.15, alpha = 0.4, size = 3, stroke = 0) +
ggplot2::xlab("tree #") +
ggplot2::ylab("Median tree leaf depth")
return(p)
} else if (which == "med.weight") {
p <-
ggplot2::ggplot(dt_depths[, median(abs(Weight)), Tree]) +
ggplot2::geom_point(ggplot2::aes(x = Tree, y = V1),
alpha = 0.4, size = 3, stroke = 0) +
ggplot2::xlab("tree #") +
ggplot2::ylab("Median absolute leaf weight")
return(p)
}
}
# Plot multiple ggplot graph aligned by rows and columns.
# ... the plots
# cols number of columns
# internal utility function
multiplot <- function(..., cols = 1) {
plots <- list(...)
num_plots <- length(plots)
layout <- matrix(seq(1, cols * ceiling(num_plots / cols)),
ncol = cols, nrow = ceiling(num_plots / cols))
if (num_plots == 1) {
print(plots[[1]])
} else {
grid::grid.newpage()
grid::pushViewport(grid::viewport(layout = grid::grid.layout(nrow(layout), ncol(layout))))
for (i in 1:num_plots) {
# Get the i,j matrix positions of the regions that contain this subplot
matchidx <- as.data.table(which(layout == i, arr.ind = TRUE))
print(
plots[[i]], vp = grid::viewport(
layout.pos.row = matchidx$row,
layout.pos.col = matchidx$col
)
)
}
}
}
globalVariables(c(
"Cluster", "ggplot", "aes", "geom_bar", "coord_flip", "xlab", "ylab", "ggtitle", "theme",
"element_blank", "element_text", "V1", "Weight"
))
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