xgb.plot.tree layout in r

Question

I was reading a xgb notebook and the xgb.plot.tree command in example result in a pic like this:

However when i do the same thing I got a pic like this which are two separate graphs and in different colors too.

Is that normal? are the two graphs two trees?

Answer 1

I have the same issue. According to an issue case on the xgboost github repository, this could be due to a change in the DiagrammeR library used by xgboost for rendering trees. https://github.com/dmlc/xgboost/issues/2640

Instead of modifying the dgr_graph object with diagrammeR commands, I chose to create a new version of the function xgb.plot.tree that defines the color of font of nodes directly. It was sufficient to add the parameter fontcolor="black" in the nodes <- DiagrammeR::create_node_df line

    xgb.plot.tree  <- function (feature_names = NULL, model = NULL, n_first_tree = NULL, 
        plot_width = NULL, plot_height = NULL, ...) 
    {

        if (class(model) != "xgb.Booster") {
            stop("model: Has to be an object of class xgb.Booster model generaged by the xgb.train function.")
        }
        if (!requireNamespace("DiagrammeR", quietly = TRUE)) {
            stop("DiagrammeR package is required for xgb.plot.tree", 
                call. = FALSE)
        }
        allTrees <- xgb.model.dt.tree(feature_names = feature_names, 
            model = model, n_first_tree = n_first_tree)
        allTrees[, `:=`(label, paste0(Feature, "\\nCover: ", Cover, 
            "\\nGain: ", Quality))]
        allTrees[, `:=`(shape, "rectangle")][Feature == "Leaf", `:=`(shape, 
            "oval")]
        allTrees[, `:=`(filledcolor, "Beige")][Feature == "Leaf", 
            `:=`(filledcolor, "Khaki")]
        nodes <- DiagrammeR::create_node_df(n = length(allTrees[, 
            ID] %>% rev), label = allTrees[, label] %>% rev, style = "filled", 
            color = "DimGray", fillcolor = allTrees[, filledcolor] %>% 
                rev, shape = allTrees[, shape] %>% rev, data = allTrees[, 
                Feature] %>% rev, fontname = "Helvetica", fontcolor="black")
        edges <- DiagrammeR::create_edge_df(from = match(allTrees[Feature != 
            "Leaf", c(ID)] %>% rep(2), allTrees[, ID] %>% rev), to = match(allTrees[Feature != 
            "Leaf", c(Yes, No)], allTrees[, ID] %>% rev), label = allTrees[Feature != 
            "Leaf", paste("<", Split)] %>% c(rep("", nrow(allTrees[Feature != 
            "Leaf"]))), color = "DimGray", arrowsize = "1.5", arrowhead = "vee", 
            fontname = "Helvetica", rel = "leading_to")
        graph <- DiagrammeR::create_graph(nodes_df = nodes, edges_df = edges)
        DiagrammeR::render_graph(graph, width = plot_width, height = plot_height)
    }

Then, it remains to change some parameters to improve the readibility of the graph. Below I add an example of the code I use to display the first tree of my xgboost model.

    xgb.plot.tree  <- function (feature_names = NULL, model = NULL, n_first_tree = NULL, 
        plot_width = NULL, plot_height = NULL, ...) 
    {

        if (class(model) != "xgb.Booster") {
            stop("model: Has to be an object of class xgb.Booster model generaged by the xgb.train function.")
        }
        if (!requireNamespace("DiagrammeR", quietly = TRUE)) {
            stop("DiagrammeR package is required for xgb.plot.tree", 
                call. = FALSE)
        }
        allTrees <- xgb.model.dt.tree(feature_names = feature_names, 
            model = model, n_first_tree = n_first_tree)

        allTrees$Quality <- round(allTrees$Quality, 3)
        allTrees$Cover <- round(allTrees$Cover, 3)


        allTrees[, `:=`(label, paste0(Feature, "\\nCover: ", Cover, 
            "\\nGain: ", Quality))]
        allTrees[, `:=`(shape, "rectangle")][Feature == "Leaf", `:=`(shape, 
            "egg")]
        allTrees[, `:=`(filledcolor, "Beige")][Feature == "Leaf", 
            `:=`(filledcolor, "Khaki")]

        nodes <- DiagrammeR::create_node_df(n = length(allTrees[, 
            ID] %>% rev), label = allTrees[, label] %>% rev, style = "filled", width=1.5,
            color = "DimGray", fillcolor = allTrees[, filledcolor] %>% 
                rev, shape = allTrees[, shape] %>% rev, data = allTrees[, 
                Feature] %>% rev, fontname = "Helvetica", fontcolor="black")

        edges <- DiagrammeR::create_edge_df(from = match(allTrees[Feature != 
            "Leaf", c(ID)] %>% rep(2), allTrees[, ID] %>% rev), to = match(allTrees[Feature != 
            "Leaf", c(Yes, No)], allTrees[, ID] %>% rev), label = allTrees[Feature != 
            "Leaf", paste("<", Split)] %>% c(rep("", nrow(allTrees[Feature != 
            "Leaf"]))), color = "DimGray", arrowsize = 1, arrowhead = "vee", minlen="5",
            fontname = "Helvetica", rel = "leading_to", fontsize="15")

        graph <- DiagrammeR::create_graph(nodes_df = nodes, edges_df = edges, attr_theme=NULL)
        DiagrammeR::render_graph(graph, width = plot_width, height = plot_height)
        return(graph)
}