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Plotly Dendrograms¤

The PlotlyDendrogram Class¤

PlotlyDendrogram pydantic-model ¤

Bases: BaseModel

PlotlyDendrogram.

Typical usage:

from lexos.cluster import PlotlyDendrogram

dendrogram = PlotlyDendrogram(dtm)
dendrogram.show()

Needs some work in returning the figure as a figure
and html and html div.

Config:

  • arbitrary_types_allowed: True

Fields:

Source code in lexos/cluster/plotly_dendrogram.py 
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class PlotlyDendrogram(BaseModel):
    """PlotlyDendrogram.

    Typical usage:

    ```python
    from lexos.cluster import PlotlyDendrogram

    dendrogram = PlotlyDendrogram(dtm)
    dendrogram.show()

    Needs some work in returning the figure as a figure
    and html and html div.
    ```
    """

    dtm: Optional[ArrayLike | DTM | pd.DataFrame] = Field(
        None, json_schema_extra={"The document-term matrix."}
    )
    labels: Optional[list[str]] = Field(
        None, description="The labels for the dendrogram."
    )
    metric: Optional[str] = Field(
        "euclidean", description="The metric to use for the dendrogram."
    )
    method: Optional[str] = Field(
        "average", description="The method to use for the dendrogram."
    )
    truncate_mode: Optional[str] = Field(
        None, description="The truncate mode for the dendrogram."
    )
    get_leaves: Optional[bool] = Field(
        True, description="The get leaves for the dendrogram."
    )
    orientation: Optional[str] = Field(
        "bottom", description="The orientation for the dendrogram."
    )
    title: Optional[str] = Field(None, description="The title for the dendrogram.")
    figsize: Optional[tuple] = Field(
        (10, 10), description="The figsize for the dendrogram."
    )
    colorscale: Optional[list] = Field(
        None, description="The colorscale for the dendrogram."
    )
    hovertext: Optional[list] = Field(
        None, description="The hovertext for the dendrogram."
    )
    color_threshold: Optional[float] = Field(
        None, description="The color threshold for the dendrogram."
    )
    config: Optional[dict] = Field(
        dict(
            displaylogo=False,
            modeBarButtonsToRemove=["toggleSpikelines"],
            scrollZoom=True,
        ),
        description="The config for the dendrogram.",
    )
    x_tickangle: Optional[int] = Field(
        0, description="The x tickangle for the dendrogram."
    )
    y_tickangle: Optional[int] = Field(
        0, description="The y tickangle for the dendrogram."
    )
    fig: Optional[Figure] = Field(None, description="The figure for the dendrogram.")
    layout: Optional[dict] = Field(
        {},
        description="The layout for the dendrogram. Keywords and values to be passed to plotly.graph_objects.Figure.update_layout().",
    )

    model_config = ConfigDict(arbitrary_types_allowed=True)

    def __init__(self, **data):
        """Initialize the PlotlyDendrogram instance."""
        super().__init__(**data)

        def distfun(x: ArrayLike) -> ArrayLike:
            """Get the pairwise distance matrix.

            Args:
                x (ArrayLike): The distance matrix.

            Returns:
                ArrayLike: The pairwise distance matrix.
            """
            return pdist(x, metric=self.metric)

        def linkagefun(x: ArrayLike) -> ArrayLike:
            """Get the hierarchical clustering encoded as a linkage matrix.

            Args:
                x (ArrayLike): The pairwise distance matrix.

            Returns:
                ArrayLike: The linkage matrix.
            """
            return sch.linkage(x, self.method)

        # Ensure there is a document-term matrix
        if self.dtm is None:
            raise LexosException("You must provide a document-term matrix.")

        # Get the matrix based on the data type
        matrix = self._get_valid_matrix()

        # Ensure there are labels (moved after matrix validation to get correct shape)
        if not self.labels:
            if isinstance(self.dtm, DTM):
                self.labels = self.dtm.labels
            elif isinstance(self.dtm, pd.DataFrame):
                # Corrected to use index for labels, as rows are documents after transpose
                self.labels = self.dtm.index.tolist()
            else:  # If matrix is a numpy array or list (now handled by _get_valid_matrix converting to numpy)
                self.labels = [f"Doc{i + 1}" for i in range(matrix.shape[0])]

        # Create the figure
        self.fig = create_dendrogram(
            matrix,
            labels=self.labels,
            distfun=distfun,
            linkagefun=linkagefun,
            orientation=self.orientation,
            colorscale=self.colorscale,
            hovertext=self.hovertext,
            color_threshold=self.color_threshold,
        )

        # Set the standard layout
        self.fig.update_layout(
            margin=dict(l=0, r=0, b=0, t=0, pad=0),
            hovermode="x",
            paper_bgcolor="rgba(0, 0, 0, 0)",
            plot_bgcolor="rgba(0, 0, 0, 0)",
            xaxis=dict(
                showline=False, ticks="", tickangle=self.x_tickangle, automargin=True
            ),
            yaxis=dict(
                showline=False, ticks="", tickangle=self.y_tickangle, automargin=True
            ),
        )

        # Set the title
        if self.title is not None:
            title = dict(
                text=self.title, x=0.5, y=0.95, xanchor="center", yanchor="top"
            )
            self.fig.update_layout(title=title, margin=dict(t=40))

        # Add user-configured layout
        self.fig.update_layout(self.layout)

        # Hack to ensure that leaves on the edge of the plot are not clipped.
        # Only works for bottom and left orientation.
        # Add an invisible scatter point to extend the margin.
        if self.orientation in ["bottom", "left"]:
            x_value = max([max(data["x"]) for data in self.fig.data])
            dummy_scatter = Scatter(
                x=[x_value], y=[0], mode="markers", opacity=0, hoverinfo="skip"
            )
            self.fig.add_trace(trace=dummy_scatter)

        # Move labels for top and right orientation
        if self.orientation == "top":
            self.fig.update_xaxes(side="top")
        if self.orientation == "right":
            self.fig.update_yaxes(side="right")

        plt.close()

    def _get_valid_matrix(self):
        """Get a valid matrix based on the data type of the dtm."""  # End of _get_valid_matrix docstring
        if isinstance(self.dtm, DTM):
            matrix = self.dtm.to_df()
            matrix.index.name = "terms"
            matrix = matrix.T
        elif isinstance(self.dtm, list):  # Added handling for list input
            matrix = np.array(self.dtm)  # Convert list to numpy array
        else:
            matrix = self.dtm

        # Now, `matrix` will always be a pandas DataFrame or a numpy array when we check `shape`
        if matrix.shape[0] < 2:
            raise LexosException(
                "The document-term matrix must have more than one document."
            )
        return matrix

    def show(self) -> None:
        """Show the figure."""  # End of show docstring
        if self.fig is None:
            raise LexosException(
                "You must call the instance before showing the figure."
            )
        self.fig.show(config=self.config)

    def to_html(self, **kwargs):
        """Create an HTML representation of the figure.

        Wrapper from the Plotly Figure to_html method.
        See https://plotly.com/python-api-reference/generated/plotly.graph_objects.Figure.html.
        """  # End of to_html docstring
        if self.fig is None:
            raise LexosException("You must call the instance before generating HTML.")
        return self.fig.to_html(**kwargs)

    def to_image(self, **kwargs):
        """Create a static image of the figure.

        Wrapper from the Plotly Figure to_image method.
        See https://plotly.com/python-api-reference/generated/plotly.graph_objects.Figure.html.
        """  # End of to_image docstring
        if self.fig is None:
            raise LexosException(
                "You must call the instance before generating an image."
            )
        return self.fig.to_image(**kwargs)

    @validate_call(config=model_config)
    def write_html(self, path: Path | str, **kwargs):
        """Save an HTML representation of the figure to disk.

        Wrapper from the Plotly Figure write_html method.
        See https://plotly.com/python-api-reference/generated/plotly.graph_objects.Figure.html.
        """
        if self.fig is None:
            raise LexosException("You must call the instance before saving the figure.")
        # Removed: if "file" in kwargs: kwargs["file"] = path
        self.fig.write_html(
            str(path), **kwargs
        )  # Convert path to string for write_html

    @validate_call(config=model_config)
    def write_image(self, path: Path | str, **kwargs):
        """Save a static image of the figure to disk.

        Wrapper from the Plotly Figure write_image method.
        See https://plotly.com/python-api-reference/generated/plotly.graph_objects.Figure.html.
        """
        if self.fig is None:
            raise LexosException("You must call the instance before saving the figure.")
        # Removed: if "file" in kwargs: kwargs["file"] = path
        self.fig.write_image(
            str(path), **kwargs
        )  # Convert path to string for write_image

color_threshold: Optional[float] = None pydantic-field ¤

The color threshold for the dendrogram.

colorscale: Optional[list] = None pydantic-field ¤

The colorscale for the dendrogram.

config: Optional[dict] = dict(displaylogo=False, modeBarButtonsToRemove=['toggleSpikelines'], scrollZoom=True) pydantic-field ¤

The config for the dendrogram.

figsize: Optional[tuple] = (10, 10) pydantic-field ¤

The figsize for the dendrogram.

get_leaves: Optional[bool] = True pydantic-field ¤

The get leaves for the dendrogram.

hovertext: Optional[list] = None pydantic-field ¤

The hovertext for the dendrogram.

labels: Optional[list[str]] = None pydantic-field ¤

The labels for the dendrogram.

layout: Optional[dict] = {} pydantic-field ¤

The layout for the dendrogram. Keywords and values to be passed to plotly.graph_objects.Figure.update_layout().

method: Optional[str] = 'average' pydantic-field ¤

The method to use for the dendrogram.

metric: Optional[str] = 'euclidean' pydantic-field ¤

The metric to use for the dendrogram.

orientation: Optional[str] = 'bottom' pydantic-field ¤

The orientation for the dendrogram.

title: Optional[str] = None pydantic-field ¤

The title for the dendrogram.

truncate_mode: Optional[str] = None pydantic-field ¤

The truncate mode for the dendrogram.

x_tickangle: Optional[int] = 0 pydantic-field ¤

The x tickangle for the dendrogram.

y_tickangle: Optional[int] = 0 pydantic-field ¤

The y tickangle for the dendrogram.

__init__(**data) ¤

Initialize the PlotlyDendrogram instance.

Source code in lexos/cluster/plotly_dendrogram.py 
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def __init__(self, **data):
    """Initialize the PlotlyDendrogram instance."""
    super().__init__(**data)

    def distfun(x: ArrayLike) -> ArrayLike:
        """Get the pairwise distance matrix.

        Args:
            x (ArrayLike): The distance matrix.

        Returns:
            ArrayLike: The pairwise distance matrix.
        """
        return pdist(x, metric=self.metric)

    def linkagefun(x: ArrayLike) -> ArrayLike:
        """Get the hierarchical clustering encoded as a linkage matrix.

        Args:
            x (ArrayLike): The pairwise distance matrix.

        Returns:
            ArrayLike: The linkage matrix.
        """
        return sch.linkage(x, self.method)

    # Ensure there is a document-term matrix
    if self.dtm is None:
        raise LexosException("You must provide a document-term matrix.")

    # Get the matrix based on the data type
    matrix = self._get_valid_matrix()

    # Ensure there are labels (moved after matrix validation to get correct shape)
    if not self.labels:
        if isinstance(self.dtm, DTM):
            self.labels = self.dtm.labels
        elif isinstance(self.dtm, pd.DataFrame):
            # Corrected to use index for labels, as rows are documents after transpose
            self.labels = self.dtm.index.tolist()
        else:  # If matrix is a numpy array or list (now handled by _get_valid_matrix converting to numpy)
            self.labels = [f"Doc{i + 1}" for i in range(matrix.shape[0])]

    # Create the figure
    self.fig = create_dendrogram(
        matrix,
        labels=self.labels,
        distfun=distfun,
        linkagefun=linkagefun,
        orientation=self.orientation,
        colorscale=self.colorscale,
        hovertext=self.hovertext,
        color_threshold=self.color_threshold,
    )

    # Set the standard layout
    self.fig.update_layout(
        margin=dict(l=0, r=0, b=0, t=0, pad=0),
        hovermode="x",
        paper_bgcolor="rgba(0, 0, 0, 0)",
        plot_bgcolor="rgba(0, 0, 0, 0)",
        xaxis=dict(
            showline=False, ticks="", tickangle=self.x_tickangle, automargin=True
        ),
        yaxis=dict(
            showline=False, ticks="", tickangle=self.y_tickangle, automargin=True
        ),
    )

    # Set the title
    if self.title is not None:
        title = dict(
            text=self.title, x=0.5, y=0.95, xanchor="center", yanchor="top"
        )
        self.fig.update_layout(title=title, margin=dict(t=40))

    # Add user-configured layout
    self.fig.update_layout(self.layout)

    # Hack to ensure that leaves on the edge of the plot are not clipped.
    # Only works for bottom and left orientation.
    # Add an invisible scatter point to extend the margin.
    if self.orientation in ["bottom", "left"]:
        x_value = max([max(data["x"]) for data in self.fig.data])
        dummy_scatter = Scatter(
            x=[x_value], y=[0], mode="markers", opacity=0, hoverinfo="skip"
        )
        self.fig.add_trace(trace=dummy_scatter)

    # Move labels for top and right orientation
    if self.orientation == "top":
        self.fig.update_xaxes(side="top")
    if self.orientation == "right":
        self.fig.update_yaxes(side="right")

    plt.close()

show() -> None ¤

Show the figure.

Source code in lexos/cluster/plotly_dendrogram.py 
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def show(self) -> None:
    """Show the figure."""  # End of show docstring
    if self.fig is None:
        raise LexosException(
            "You must call the instance before showing the figure."
        )
    self.fig.show(config=self.config)

to_html(**kwargs) ¤

Create an HTML representation of the figure.

Wrapper from the Plotly Figure to_html method. See https://plotly.com/python-api-reference/generated/plotly.graph_objects.Figure.html.

Source code in lexos/cluster/plotly_dendrogram.py 
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def to_html(self, **kwargs):
    """Create an HTML representation of the figure.

    Wrapper from the Plotly Figure to_html method.
    See https://plotly.com/python-api-reference/generated/plotly.graph_objects.Figure.html.
    """  # End of to_html docstring
    if self.fig is None:
        raise LexosException("You must call the instance before generating HTML.")
    return self.fig.to_html(**kwargs)

to_image(**kwargs) ¤

Create a static image of the figure.

Wrapper from the Plotly Figure to_image method. See https://plotly.com/python-api-reference/generated/plotly.graph_objects.Figure.html.

Source code in lexos/cluster/plotly_dendrogram.py 
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def to_image(self, **kwargs):
    """Create a static image of the figure.

    Wrapper from the Plotly Figure to_image method.
    See https://plotly.com/python-api-reference/generated/plotly.graph_objects.Figure.html.
    """  # End of to_image docstring
    if self.fig is None:
        raise LexosException(
            "You must call the instance before generating an image."
        )
    return self.fig.to_image(**kwargs)

write_html(path: Path | str, **kwargs) ¤

Save an HTML representation of the figure to disk.

Wrapper from the Plotly Figure write_html method. See https://plotly.com/python-api-reference/generated/plotly.graph_objects.Figure.html.

Source code in lexos/cluster/plotly_dendrogram.py 
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@validate_call(config=model_config)
def write_html(self, path: Path | str, **kwargs):
    """Save an HTML representation of the figure to disk.

    Wrapper from the Plotly Figure write_html method.
    See https://plotly.com/python-api-reference/generated/plotly.graph_objects.Figure.html.
    """
    if self.fig is None:
        raise LexosException("You must call the instance before saving the figure.")
    # Removed: if "file" in kwargs: kwargs["file"] = path
    self.fig.write_html(
        str(path), **kwargs
    )  # Convert path to string for write_html

write_image(path: Path | str, **kwargs) ¤

Save a static image of the figure to disk.

Wrapper from the Plotly Figure write_image method. See https://plotly.com/python-api-reference/generated/plotly.graph_objects.Figure.html.

Source code in lexos/cluster/plotly_dendrogram.py 
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@validate_call(config=model_config)
def write_image(self, path: Path | str, **kwargs):
    """Save a static image of the figure to disk.

    Wrapper from the Plotly Figure write_image method.
    See https://plotly.com/python-api-reference/generated/plotly.graph_objects.Figure.html.
    """
    if self.fig is None:
        raise LexosException("You must call the instance before saving the figure.")
    # Removed: if "file" in kwargs: kwargs["file"] = path
    self.fig.write_image(
        str(path), **kwargs
    )  # Convert path to string for write_image

rendering:
  show_root_heading: true
  heading_level: 3

__init__(**data) ¤

Initialize the PlotlyDendrogram instance.

Source code in lexos/cluster/plotly_dendrogram.py 
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def __init__(self, **data):
    """Initialize the PlotlyDendrogram instance."""
    super().__init__(**data)

    def distfun(x: ArrayLike) -> ArrayLike:
        """Get the pairwise distance matrix.

        Args:
            x (ArrayLike): The distance matrix.

        Returns:
            ArrayLike: The pairwise distance matrix.
        """
        return pdist(x, metric=self.metric)

    def linkagefun(x: ArrayLike) -> ArrayLike:
        """Get the hierarchical clustering encoded as a linkage matrix.

        Args:
            x (ArrayLike): The pairwise distance matrix.

        Returns:
            ArrayLike: The linkage matrix.
        """
        return sch.linkage(x, self.method)

    # Ensure there is a document-term matrix
    if self.dtm is None:
        raise LexosException("You must provide a document-term matrix.")

    # Get the matrix based on the data type
    matrix = self._get_valid_matrix()

    # Ensure there are labels (moved after matrix validation to get correct shape)
    if not self.labels:
        if isinstance(self.dtm, DTM):
            self.labels = self.dtm.labels
        elif isinstance(self.dtm, pd.DataFrame):
            # Corrected to use index for labels, as rows are documents after transpose
            self.labels = self.dtm.index.tolist()
        else:  # If matrix is a numpy array or list (now handled by _get_valid_matrix converting to numpy)
            self.labels = [f"Doc{i + 1}" for i in range(matrix.shape[0])]

    # Create the figure
    self.fig = create_dendrogram(
        matrix,
        labels=self.labels,
        distfun=distfun,
        linkagefun=linkagefun,
        orientation=self.orientation,
        colorscale=self.colorscale,
        hovertext=self.hovertext,
        color_threshold=self.color_threshold,
    )

    # Set the standard layout
    self.fig.update_layout(
        margin=dict(l=0, r=0, b=0, t=0, pad=0),
        hovermode="x",
        paper_bgcolor="rgba(0, 0, 0, 0)",
        plot_bgcolor="rgba(0, 0, 0, 0)",
        xaxis=dict(
            showline=False, ticks="", tickangle=self.x_tickangle, automargin=True
        ),
        yaxis=dict(
            showline=False, ticks="", tickangle=self.y_tickangle, automargin=True
        ),
    )

    # Set the title
    if self.title is not None:
        title = dict(
            text=self.title, x=0.5, y=0.95, xanchor="center", yanchor="top"
        )
        self.fig.update_layout(title=title, margin=dict(t=40))

    # Add user-configured layout
    self.fig.update_layout(self.layout)

    # Hack to ensure that leaves on the edge of the plot are not clipped.
    # Only works for bottom and left orientation.
    # Add an invisible scatter point to extend the margin.
    if self.orientation in ["bottom", "left"]:
        x_value = max([max(data["x"]) for data in self.fig.data])
        dummy_scatter = Scatter(
            x=[x_value], y=[0], mode="markers", opacity=0, hoverinfo="skip"
        )
        self.fig.add_trace(trace=dummy_scatter)

    # Move labels for top and right orientation
    if self.orientation == "top":
        self.fig.update_xaxes(side="top")
    if self.orientation == "right":
        self.fig.update_yaxes(side="right")

    plt.close()

rendering:
  show_root_heading: true
  heading_level: 3

_get_valid_matrix() ¤

Get a valid matrix based on the data type of the dtm.

Source code in lexos/cluster/plotly_dendrogram.py 
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def _get_valid_matrix(self):
    """Get a valid matrix based on the data type of the dtm."""  # End of _get_valid_matrix docstring
    if isinstance(self.dtm, DTM):
        matrix = self.dtm.to_df()
        matrix.index.name = "terms"
        matrix = matrix.T
    elif isinstance(self.dtm, list):  # Added handling for list input
        matrix = np.array(self.dtm)  # Convert list to numpy array
    else:
        matrix = self.dtm

    # Now, `matrix` will always be a pandas DataFrame or a numpy array when we check `shape`
    if matrix.shape[0] < 2:
        raise LexosException(
            "The document-term matrix must have more than one document."
        )
    return matrix

rendering:
  show_root_heading: true
  heading_level: 3

show() -> None ¤

Show the figure.

Source code in lexos/cluster/plotly_dendrogram.py 
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def show(self) -> None:
    """Show the figure."""  # End of show docstring
    if self.fig is None:
        raise LexosException(
            "You must call the instance before showing the figure."
        )
    self.fig.show(config=self.config)

rendering:
  show_root_heading: true
  heading_level: 3

to_html(**kwargs) ¤

Create an HTML representation of the figure.

Wrapper from the Plotly Figure to_html method. See https://plotly.com/python-api-reference/generated/plotly.graph_objects.Figure.html.

Source code in lexos/cluster/plotly_dendrogram.py 
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def to_html(self, **kwargs):
    """Create an HTML representation of the figure.

    Wrapper from the Plotly Figure to_html method.
    See https://plotly.com/python-api-reference/generated/plotly.graph_objects.Figure.html.
    """  # End of to_html docstring
    if self.fig is None:
        raise LexosException("You must call the instance before generating HTML.")
    return self.fig.to_html(**kwargs)

rendering:
  show_root_heading: true
  heading_level: 3

to_image(**kwargs) ¤

Create a static image of the figure.

Wrapper from the Plotly Figure to_image method. See https://plotly.com/python-api-reference/generated/plotly.graph_objects.Figure.html.

Source code in lexos/cluster/plotly_dendrogram.py 
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def to_image(self, **kwargs):
    """Create a static image of the figure.

    Wrapper from the Plotly Figure to_image method.
    See https://plotly.com/python-api-reference/generated/plotly.graph_objects.Figure.html.
    """  # End of to_image docstring
    if self.fig is None:
        raise LexosException(
            "You must call the instance before generating an image."
        )
    return self.fig.to_image(**kwargs)

rendering:
  show_root_heading: true
  heading_level: 3

write_html(path: Path | str, **kwargs) ¤

Save an HTML representation of the figure to disk.

Wrapper from the Plotly Figure write_html method. See https://plotly.com/python-api-reference/generated/plotly.graph_objects.Figure.html.

Source code in lexos/cluster/plotly_dendrogram.py 
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@validate_call(config=model_config)
def write_html(self, path: Path | str, **kwargs):
    """Save an HTML representation of the figure to disk.

    Wrapper from the Plotly Figure write_html method.
    See https://plotly.com/python-api-reference/generated/plotly.graph_objects.Figure.html.
    """
    if self.fig is None:
        raise LexosException("You must call the instance before saving the figure.")
    # Removed: if "file" in kwargs: kwargs["file"] = path
    self.fig.write_html(
        str(path), **kwargs
    )  # Convert path to string for write_html

rendering:
  show_root_heading: true
  heading_level: 3

write_image(path: Path | str, **kwargs) ¤

Save a static image of the figure to disk.

Wrapper from the Plotly Figure write_image method. See https://plotly.com/python-api-reference/generated/plotly.graph_objects.Figure.html.

Source code in lexos/cluster/plotly_dendrogram.py 
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@validate_call(config=model_config)
def write_image(self, path: Path | str, **kwargs):
    """Save a static image of the figure to disk.

    Wrapper from the Plotly Figure write_image method.
    See https://plotly.com/python-api-reference/generated/plotly.graph_objects.Figure.html.
    """
    if self.fig is None:
        raise LexosException("You must call the instance before saving the figure.")
    # Removed: if "file" in kwargs: kwargs["file"] = path
    self.fig.write_image(
        str(path), **kwargs
    )  # Convert path to string for write_image

rendering:
  show_root_heading: true
  heading_level: 3