PDSUtilities 0.0.5

Utilities for data science in python

PDSUtilities

Python Data Science Utilities

Installation

You can install PDSUtilities using pip:

pip install PDSUtilities

or by adding PDSUtilities to your requirements.txt file.

Usage

Import the functions you need as follows:

from PBSUtilities.xgboost import plot_importance
from PBSUtilities.xgboost import plot_tree

See below for sample usage of both of these functions.

Functions

Function: plot_importance()

The plot_importane() function is a plotly-based replacement for xgboost.plot_importance(). The APIs are similar (though several parameters have been renamed) but with two key differences. First, PDSUtilities.xgboost.plot_importance() does not rely on fmap to supply feature names, instead exposing a features parameter that that can either be a list of feature names or a dict that allows mapping of feature names. And second, PDSUtilities.xgboost.plot_importance() does not rely on matplotlib at all, instead using plotly for visualisation. This produces an interactive, publication-quality visualisation that can also be customised more easily, particularly using plotly.io templates.

The PDSUtilities.xgboost.plot_importance() function is a direct copy/paste/edit modification of xgboost.plot_importance() with a few minor tweaks to the API and relatively light changes to the code. The xgboost team deserves the vast majority of credit for this code! The xgboost license can be found here: https://github.com/dmlc/xgboost/blob/master/LICENSE

The API is:

plot_importance(
	booster, features = {}, width = 0.6, xrange = None, yrange = None,
	title = 'Feature Importance', xlabel = 'F Score', ylabel = 'Features',
	fmap = '', max_features = None, importance_type = 'weight',
	show_grid = True, show_values = True)

Example Usage

import pandas as pd

from xgboost import XGBClassifier
from xgboost import XGBModel
from xgboost import Booster

from sklearn.compose import ColumnTransformer
from sklearn.feature_selection import chi2
from sklearn.feature_selection import SelectKBest
from sklearn.model_selection import train_test_split
from sklearn.pipeline import Pipeline
from sklearn.preprocessing import OrdinalEncoder
from sklearn.preprocessing import MinMaxScaler

from PDSUtilities.xgboost import plot_importance

[...]

df = pd.read_csv("/some/datafile.csv")

xt, xv, yt, yv = train_test_split(
	df.drop("OutputFeature", axis = 1),
	df["OutputFeature"],
)

pipeline = Pipeline(steps = [
    ("transform", ColumnTransformer(
            transformers = [
                ("cat", OrdinalEncoder(), categorical_columns),
                ("num", MinMaxScaler(), numerical_columns)
            ]
        )
    ),
    ("features", SelectKBest()),
    ("classifier", XGBClassifier(
            objective = "binary:logistic",
			eval_metric = "auc",
			use_label_encoder = False
        )
    )
])

parameters = {
    "classifier__colsample_bytree": 0.2,
    "classifier__gamma": 0.4,
    "classifier__learning_rate": 0.1,
    "classifier__max_depth": 4,
    "classifier__n_estimators": 60,
    "features__k": 10,
    "features__score_func": chi2
}
pipeline.set_params(**parameters)
model = pipeline.fit(xt, yt)

[...]

classifier = pipeline["classifier"]
features = [feature for column in xt.columns]

fig = plot_importance(classifier, features = features)
fig.update_layout(template = "presentation", width = 700, height = 600)
fig.show()

Function: plot_tree()

The plot_tree() function is a plotly-based replacement for xgboost.plot_tree() that takes visualising booster trees to a whole new visual level. As a result, the API looks nothing like that of xgboost.plot_tree(), though in its simplest usage, it is almost identical, though again not requiring fmap for adding feature names to the visualisation:

from PDSUtilities.xgboost import plot_tree

[...]

booster = pipeline["classifier"].get_booster()

fig = plot_tree(booster, tree = 0, features = features)
fig.show()

In this example, tree is the tree number and, as with plot_importance(), the features parameter can be either a list or a dict.

Note that the default colours were chosen from a vibrant, colourblind-friendly palette, but can be completely configured via a number of additional configuration settings. An additional, handy parameter is grayscale = True, which produces a also colorblind-friendly, grayscale visualisation.

Finally, the Figure object returned by plot_impotance() can be further customised via plotly's extensive API.

Example The overall font can be configured by any of the following settings:

font = {
	'family': "Garamond, Cambria, Arial, etc",
	'size': 16,
	'color': "#000000"
}

These settings can be overridden for nodes, leaves and edges by the node_font, leaf_font and edge_font settings, respectively. For example, specifying

edge_font = {
	'size': 11,
}

would override the font setting so that the edge labels would be 11pt Garamond.

Edge colours can be configured via a decision-specific dict. For example, the edge colours corresponding to grayscale = True could be set by:

edge_clours = {
	'Yes': "#222222",
	'No': "#777777",
	'Missing': "#AAAAAA",
	'Yes/Missing':  "#222222",
	'No/Missing': "#777777",
}

Note that the keys Yes/Missing and No/Missing correspond to the case where a branch point has a Missing branch that connects to the same child as Yes or No, respectively.

Similarly, the edge labels can also be configured via a decision-specific dict. The default is:

edge_labels = {
	'Yes': "Yes",
	'No': "No",
	'Missing': "Missing",
	'Yes/Missing': "Yes/Missing",
	'No/Missing': "No/Missing"
}

This is handy, for example, when it is known a priori that there are no missing values, in which case setting

edge_labels = {
	'Yes/Missing': "Yes/Missing",
	'No/Missing': "No/Missing"
}

will lead to a much cleaner looking visualisation.

Node and leaf shapes and lines can also be configured:

 node_shape = {
	'type': "rect",
	'fillcolor': "#CBCBCB",
	'opacity': 1.0,
}
node_line = {
	'color': "#666666",
	'width': 1,
	'dash': "solid",
}
leaf_shape = {
	'type': "rounded",
	'fillcolor': "#EDEDED",
	'opacity': 1.0,
}
leaf_line = {
	'color': "#777777",
	'width': 1,
	'dash': "solid",
}

Note that type can be any of "rect", "circle" or "rounded" and that dash can be any of "solid", "dot", "dash", "longdash", "dashdot" or "longdashdot".

The edge line, arrow and label properties can also be configured:

edge_line = {
	'width': 1.5,
	'dash': "solid",
}
edge_arrow = {
	'arrowhead': 3, # Integer between or equal to 0 and 8
	'arrowsize': 1.5,
}
edge_label = {
	'align': "center",
	'bgcolor': "#FFFFFF",
	'bordercolor': "rgba(0,0,0,0)",
	'borderpad': 1,
	'borderwidth': 1,
	'opacity': 1.0,
	'textangle': 0,
	'valign': "middle",
	'visible': True,
}

where dash is as above and arrowhead is an int in range(0, 9) that specifies the arrowhead style.

Additionally, plot_tree() accepts width and height parameters specifying the overall width and height of the visualisation--though the defaults are reasonably good and tree-size dependent--as well as a precision parameter specifying the number of decimal places displayed when rendering the numbers in nodes and leaves.

Finally, plot_tree() also accepts a scale parameter that can be adjusted up or down if the node and/or leaf labels do not quite fit in their corresponding shapes. This can occur because plot_tree() does not use font metrics for computing the size of the labels, instead using a reasonable guess. This is because plotly does not offer this via their API and no python font metric libraries seemed to offer what was needed. This may be improved in the future but for now, adjusting scale is the preferred method for dealing with this.

As with plot_impotance() the returned Figure object can be further customised via plotly's extensive API.

The plot_tree() API is:

def plot_tree(booster, tree, features = {}, width = None, height = None,
    precision = 4, scale = 0.7, font = None, grayscale = False,
    node_shape = {}, node_line = {}, node_font = {},
    leaf_shape = {}, leaf_line = {}, leaf_font = {},
    edge_labels = {}, edge_colors = {}, edge_arrow = {},
    edge_line = {}, edge_label = {}, edge_font = {}):