[R] Allow passing data.frame to SHAP (dmlc#10744)

Author: david-cortes

R-package/R/xgb.ggplot.R

@@ -102,6 +102,27 @@ xgb.ggplot.deepness <- function(model = NULL, which = c("2x1", "max.depth", "med
 #' @export
 xgb.ggplot.shap.summary <- function(data, shap_contrib = NULL, features = NULL, top_n = 10, model = NULL,
                                     trees = NULL, target_class = NULL, approxcontrib = FALSE, subsample = NULL) {
+  if (inherits(data, "xgb.DMatrix")) {
+    stop(
+      "'xgb.ggplot.shap.summary' is not compatible with 'xgb.DMatrix' objects. Try passing a matrix or data.frame."
+    )
+  }
+  cols_categ <- NULL
+  if (!is.null(model)) {
+    ftypes <- getinfo(model, "feature_type")
+    if (NROW(ftypes)) {
+      if (length(ftypes) != ncol(data)) {
+        stop(sprintf("'data' has incorrect number of columns (expected: %d, got: %d).", length(ftypes), ncol(data)))
+      }
+      cols_categ <- colnames(data)[ftypes == "c"]
+    }
+  } else if (inherits(data, "data.frame")) {
+    cols_categ <- names(data)[sapply(data, function(x) is.factor(x) || is.character(x))]
+  }
+  if (NROW(cols_categ)) {
+    warning("Categorical features are ignored in 'xgb.ggplot.shap.summary'.")
+  }
+
   data_list <- xgb.shap.data(
     data = data,
     shap_contrib = shap_contrib,
@@ -114,6 +135,10 @@ xgb.ggplot.shap.summary <- function(data, shap_contrib = NULL, features = NULL,
     subsample = subsample,
     max_observations = 10000  # 10,000 samples per feature.
   )
+  if (NROW(cols_categ)) {
+    data_list <- lapply(data_list, function(x) x[, !(colnames(x) %in% cols_categ), drop = FALSE])
+  }
+
   p_data <- prepare.ggplot.shap.data(data_list, normalize = TRUE)
   # Reverse factor levels so that the first level is at the top of the plot
   p_data[, "feature" := factor(feature, rev(levels(feature)))]
@@ -134,7 +159,8 @@ xgb.ggplot.shap.summary <- function(data, shap_contrib = NULL, features = NULL,
 #' @param data_list The result of `xgb.shap.data()`.
 #' @param normalize Whether to standardize feature values to mean 0 and
 #'   standard deviation 1. This is useful for comparing multiple features on the same
-#'   plot. Default is `FALSE`.
+#'   plot. Default is `FALSE`. Note that it cannot be used when the data contains
+#'   categorical features.
 #' @return A `data.table` containing the observation ID, the feature name, the
 #'   feature value (normalized if specified), and the SHAP contribution value.
 #' @noRd

R-package/R/xgb.plot.shap.R

@@ -2,7 +2,7 @@
 #'
 #' Visualizes SHAP values against feature values to gain an impression of feature effects.
 #'
-#' @param data The data to explain as a `matrix` or `dgCMatrix`.
+#' @param data The data to explain as a `matrix`, `dgCMatrix`, or `data.frame`.
 #' @param shap_contrib Matrix of SHAP contributions of `data`.
 #'   The default (`NULL`) computes it from `model` and `data`.
 #' @param features Vector of column indices or feature names to plot. When `NULL`
@@ -285,8 +285,11 @@ xgb.plot.shap.summary <- function(data, shap_contrib = NULL, features = NULL, to
 xgb.shap.data <- function(data, shap_contrib = NULL, features = NULL, top_n = 1, model = NULL,
                           trees = NULL, target_class = NULL, approxcontrib = FALSE,
                           subsample = NULL, max_observations = 100000) {
-  if (!is.matrix(data) && !inherits(data, "dgCMatrix"))
-    stop("data: must be either matrix or dgCMatrix")
+  if (!inherits(data, c("matrix", "dsparseMatrix", "data.frame")))
+    stop("data: must be matrix, sparse matrix, or data.frame.")
+  if (inherits(data, "data.frame") && length(class(data)) > 1L) {
+    data <- as.data.frame(data)
+  }
 
   if (is.null(shap_contrib) && (is.null(model) || !inherits(model, "xgb.Booster")))
     stop("when shap_contrib is not provided, one must provide an xgb.Booster model")
@@ -311,7 +314,14 @@ xgb.shap.data <- function(data, shap_contrib = NULL, features = NULL, top_n = 1,
     stop("if model has no feature_names, columns in `data` must match features in model")
 
   if (!is.null(subsample)) {
-    idx <- sample(x = seq_len(nrow(data)), size = as.integer(subsample * nrow(data)), replace = FALSE)
+    if (subsample <= 0 || subsample >= 1) {
+      stop("'subsample' must be a number between zero and one (non-inclusive).")
+    }
+    sample_size <- as.integer(subsample * nrow(data))
+    if (sample_size < 2) {
+      stop("Sampling fraction involves less than 2 rows.")
+    }
+    idx <- sample(x = seq_len(nrow(data)), size = sample_size, replace = FALSE)
   } else {
     idx <- seq_len(min(nrow(data), max_observations))
   }

R-package/man/xgb.plot.shap.Rd

@@ -449,6 +449,26 @@ test_that("xgb.shap.data works with subsampling", {
   expect_equal(NROW(data_list$data), NROW(data_list$shap_contrib))
 })
 
+test_that("xgb.shap.data works with data frames", {
+  data(mtcars)
+  df <- mtcars
+  df$cyl <- factor(df$cyl)
+  x <- df[, -1]
+  y <- df$mpg
+  dm <- xgb.DMatrix(x, label = y, nthread = 1L)
+  model <- xgb.train(
+    data = dm,
+    params = list(
+      max_depth = 2,
+      nthread = 1
+    ),
+    nrounds = 2
+  )
+  data_list <- xgb.shap.data(data = df[, -1], model = model, top_n = 2, subsample = 0.8)
+  expect_equal(NROW(data_list$data), as.integer(0.8 * nrow(df)))
+  expect_equal(NROW(data_list$data), NROW(data_list$shap_contrib))
+})
+
 test_that("prepare.ggplot.shap.data works", {
   .skip_if_vcd_not_available()
   data_list <- xgb.shap.data(data = sparse_matrix, model = bst.Tree, top_n = 2)
@@ -472,6 +492,44 @@ test_that("xgb.plot.shap.summary works", {
   expect_silent(xgb.ggplot.shap.summary(data = sparse_matrix, model = bst.Tree, top_n = 2))
 })
 
+test_that("xgb.plot.shap.summary ignores categorical features", {
+  .skip_if_vcd_not_available()
+  data(mtcars)
+  df <- mtcars
+  df$cyl <- factor(df$cyl)
+  levels(df$cyl) <- c("a", "b", "c")
+  x <- df[, -1]
+  y <- df$mpg
+  dm <- xgb.DMatrix(x, label = y, nthread = 1L)
+  model <- xgb.train(
+    data = dm,
+    params = list(
+      max_depth = 2,
+      nthread = 1
+    ),
+    nrounds = 2
+  )
+  expect_warning({
+    xgb.ggplot.shap.summary(data = x, model = model, top_n = 2)
+  })
+
+  x_num <- mtcars[, -1]
+  x_num$gear <- as.numeric(x_num$gear) - 1
+  x_num <- as.matrix(x_num)
+  dm <- xgb.DMatrix(x_num, label = y, feature_types = c(rep("q", 8), "c", "q"), nthread = 1L)
+  model <- xgb.train(
+    data = dm,
+    params = list(
+      max_depth = 2,
+      nthread = 1
+    ),
+    nrounds = 2
+  )
+  expect_warning({
+    xgb.ggplot.shap.summary(data = x_num, model = model, top_n = 2)
+  })
+})
+
 test_that("check.deprecation works", {
   ttt <- function(a = NNULL, DUMMY = NULL, ...) {
     check.deprecation(...)