R/example/example_dependence_plot.R

In SHAPforxgboost: SHAP Plots for 'XGBoost'

# **SHAP dependence plot**

# 1. simple dependence plot with SHAP values of x on the y axis
shap.plot.dependence(data_long = shap_long_iris, x="Petal.Length",
                     add_hist = TRUE, add_stat_cor = TRUE)

# 2. can choose a different SHAP values on the y axis
shap.plot.dependence(data_long = shap_long_iris, x="Petal.Length",
                           y = "Petal.Width")

# 3. color by another feature's feature values
shap.plot.dependence(data_long = shap_long_iris, x="Petal.Length",
                           color_feature = "Petal.Width")

# 4. choose 3 different variables for x, y, and color
shap.plot.dependence(data_long = shap_long_iris, x="Petal.Length",
                           y = "Petal.Width", color_feature = "Petal.Width")

# Optional to add hist or remove smooth line, optional to plot fewer data (make plot quicker)
shap.plot.dependence(data_long = shap_long_iris, x="Petal.Length",
                     y = "Petal.Width", color_feature = "Petal.Width",
                     add_hist = TRUE, smooth = FALSE, dilute = 3)

# to make a list of plot
plot_list <- lapply(names(iris)[2:3], shap.plot.dependence, data_long = shap_long_iris)

# **SHAP interaction effect plot **

# To get the interaction SHAP dataset for plotting, need to get `shap_int` first:
mod1 = xgboost::xgboost(
  data = as.matrix(iris[,-5]), label = iris$Species,
  gamma = 0, eta = 1, lambda = 0,nrounds = 1, verbose = FALSE, nthread = 1)
# Use either:
data_int <- shap.prep.interaction(xgb_mod = mod1,
                                  X_train = as.matrix(iris[,-5]))
# or:
shap_int <- predict(mod1, as.matrix(iris[,-5]),
                    predinteraction = TRUE)

# if data_int is supplied, y axis will plot the interaction values of y (vs. x)
shap.plot.dependence(data_long = shap_long_iris,
                           data_int = shap_int_iris,
                           x="Petal.Length",
                           y = "Petal.Width",
                           color_feature = "Petal.Width")