Skip to content

Latest commit

 

History

History
629 lines (461 loc) · 24.9 KB

API.md

File metadata and controls

629 lines (461 loc) · 24.9 KB
Raw

Basic Functions

  • load_ggplot(ggplot=None, figsize=None)

    Convert a plotnine plot object to a patchworklib.Bricks object.

    Parameters

    • ggplot: plotnine.ggplot.ggplot
    • figsize: tuple (float, float)
      Figure size. If it is not specified, the generated Bricks object will keep the original figure size of the given ggplot object.

    Returns

    patchworklib.Bricks object

  • overwrite_axisgrid()

    Overwrite the __init__ methods in seaborn.axisgrid.xxGrid classes. The function changes the figure object given in the __init__ functions of the axisgrid class objects, which is used for drawing plots, to _basefigure in the patchworklib. If you want to load the plots generated based on seaborn.axisgrid.xxGrid objects as patchworklib.Brick(s) object using load_seaborngrid function, you should execute this function in advance.

    Returns

    None

  • load_seabornobj(g, label=None, labels=None, figsize=(3, 3))

    Load a seaborn plot generated based on seaborn._core.plot.Plotter class. The method is a prototype version. By using this function, plots generated using object-oriented seaborn interface can be handled as a patchworklib.Brick(s) class object.

    Parameters

    • g: seaborn.axisgrid.xxGrid object
      A return value of the seaborn figure-level plotting functions such as relplot, distplot, catplot, jointplot, and pairplot.
    • label: str
      Unique identifier for the patchworklib.Brick(s) class object to be returned. If you want to adjust a layout composed of multiple bricks object using the label indexing method, providing the unique label name for returned object should be encouraged.
    • figsize: tuple (float, float)
      Figure size. If it is not specified, the converted Bricks object will keep the original figure size of the given seaborn plot.

    Returns

    patchworklib.Bricks object

  • load_seaborngrid(g, label=None, labels=None, figsize=None)

    Load seaborn plot generated based on seaborn.axisgrid.xxGrid class.
    In general, seaborn plots generated by figure-level function cannot be handled as subplot(s) with other matplotlib plots. However, by processing these seaborn plots via this function, you can handle them as patchworklib.Brick(s) class objects.

    Notes

    You should execute overwrite_axisgrid function before using this function.

    Parameters

    • g: seaborn.axisgrid.xxGrid object
      A return value of the seaborn figure-level plotting functions such as relplot, distplot, catplot, jointplot, and pairplot.
    • label: str
      Unique identifier for the patchworklib.Brick(s) class object to be returned. If you want to adjust a layout composed of multiple bricks object using the label indexing method, providing the unique label name for returned object should be encouraged.
    • figsize: tuple (float, float)
      Figure size. If it is not specified, the converted Bricks object will keep the original figure size of the given seaborn plot.

    Returns

    patchworklib.Bricks object

  • hstack(brick1, brick2, target=None, margin=None, direction='r', adjust_height=True, adjust_width=True, va='top')

    Align two patchworklib.Brick(s) objects horizontally. When joining two Brick(s) objects by "|" or "+" operator, this function is called internally.

    • brick1 | brick2 is identical to hstack(brick1, brick2)

    • brick1 + brick2 is identical to hstack(brick1, brick2, adjust_height=False)

    Parameters

    • brick1: patchworklib.Brick or patchworklib.Bricks class object
      A patchworklib.Brick(s) class object to be joined with brick2 object. The location of this object is used as the base position for determining the brick2 placement.
    • brick2: patchworklib.Brick or patchworklib.Bricks class object
      A patchworklib.Brick(s) class object to be placed on the side specified by direction (by default, on the right side) of the brick1 object.
    • target: str, default: None
      Unique label name of the Brick or Brick(s) object that is a part of the brick1 object. If you want to place brick2 object next to the specific Brick(s) object in brick1 object, please provide the label value of the Brick(s) object.
    • margin: float or str ("none"), default: None
      Margin size between the two given Brick(s) objects. If None, the pw.param["margin"] value will be used as the margin size. If the value is "none", two Brick(s) objects will be joined with no margin (meaning that the axes spines will be joined so that they are fully glued together).
    • direction: str ("r" or "l"), default: "r"
      Side on which brick2 is placed with respect to brick1. "r" means right. "l" means left.
    • adjust_height: bool, default: True
      If True, the height of brick2 object is adjusted so that it will be equal to the height of brick1 object.
    • adjust_width: bool, default: True
      If True, the width of brick2 will be adjusted according to the aspect of brick2 after stacking. If False, brick2 will keep its original width after stacking. If adjust_height is False, the value will also be False.
    • va: str ("top" or "bottom"), default: False
      If adjust_height is False, the value will be effective. If the value is "top", brick2 object will be aligned to the left/right top of brick1 object. If the value is "bottom", brick2 object will be aligned to the left/right bottom of brick1 object.

    Returns

    patchworlib.Bricks object

  • vstack(brick1, brick2, target=None, margin=None, direction='t', adjust_height=True, adjust_width=True, ha='l')

    Align two patchworlib.Brick(s) objects vertically. When joining two Brick(s) objects by "/" or "-" operator, this function is called internally.

    • brick2 / brick1 is identical to vstack(brick1, brick2)

    • brick2 / brick1 is identical to vstack(brick1, brick2, adjust_width=False)

    Parameters

    • brick1: patchworklib.Brick or patchworklib.Bricks class object
      A patchworlib.Brick(s) class object to be joined with brick2 object. The location of this object is used as the base position for determining the brick2 placement.
    • brick2: patchworklib.Brick or patchworklib.Bricks class object
      A patchworlib.Brick(s) class object to be placed on the side specified by direction (by default, on the top side) of the brick1 object.
    • target: str, default: None
      Unique label name of the Brick or Brick(s) object that is a part of the brick1 object. If you want to place brick2 object next to the specific Brick(s) object in brick1 object, please provide the label value of the Brick(s) object.
    • margin: flaot, default: pw.param["margin"]
      Margin size between the two given Brick(s) objects. If None, the pw.param["margin"] value would be used as the margin size. If the value is "none", two patchworlib.Brick(s) objects will be joined with no margin (meaning that the axes spines will be joined so that they are fully glued together).
    • direction: str ("t" or "b"), default: "t"
      Side on which brick2 is placed with respect to brick1. "t" means top, "b" means bottom.
    • adjust_height: bool, default: True
      If True, the height of brick2 will be adjusted according to the aspect of brick2 after stacking. If False, brick2 will keep its original height after stacking. If ajust_width is Fasle, the value will also be False.
    • adjust_width: bool, default: True
      If True, the width of brick2 object is adjusted so that it will be equal to the width of brick1 object.
    • ha: str ("left" or "right"), default: False
      If adjsut_width is False, the value will be effective. If the value is "left", brick2 object will be stacked on/below the left top/bottom of brick1 object. If the value is "right", brick2 object will be stacked on/below the right top/bottom of brick1 object.

    Returns

    patchworlib.Bricks object

  • stack(bricks, margin=None, operator='|', equal_spacing=False)

    Stack multiple Brick(s) objects horizontally or vetically.

    Parameters

    • bricks: list of patchworklib.Brick(s) objects
      List composed of patchworklib.Brick(s) objects. The list can include both patchworklib.Brick and patchworklib.Bricks objects.
    • margin: float, default: None
      Margin size of each Brick(s). If None, the pw.param["margin"] value would be used as the margin size between the Brick(s) objects.
    • operator: str (|, /, +, or -), default: |
      Orientation of the arrangement for the given patchworklib.Brick(s) object. If this value is | or /, the width/height of the object to be stacked will be adjusted so that it will be aligned with previous one.
      • equal_spacing: bool, default: False If this value is True, axes bounding-boxes should be placed with equal spacing between them. Otherwise, depending on the text values of x/y tick labels and x/y labels, they may not always be equally spaced.

    Returns

    patchworlib.Bricks object

  • inset(brick1, brick2, loc='upper right', wratio=0.4, hratio=0.4, vmargin=0.1, hmargin=0.1, alpha=0.0)

    Position the brick2 object inside the brick1 object.

    Parameters

    • brick1: patchworklib.Brick or patchworklib.Bricks class object
      Brick(s) class object to be joined with brick2 object. The location of this object is used as the base position for determining the brick2 placement.
    • brick2: patchworklib.Brick or patchworklib.Bricks class object
      Brick(s) class object to be placed in specified in brick1 object.
    • position: str, ("upper right", "lower rigtht", "upper left", "lower left") Position of brick2 object in brick1 object.
    • wratio: float, default: 0.1
      Ratio of the brick2 width to brick1 object.
    • hratio: float, default: 0.1
      Ratio of the brick2 height to brick1 object.
    • vmargin: float, default: 0.1
      Margin from the bottom/top.
    • hmargin: float, default: 0.1
      Margin from the right/left.
    • alpha: flaot, default: 0.0
      Alpha of background of brick2 object

    Returns

    patchworlib.Bricks object

  • expand(bricks, w, h)

    Expand the size of the bricks object.

    Parameters

    • bricks: patchworklib.Bricks object
      A patchworlib.Brick(s) object to be expand.
    • w: int or float
      Expansion ratio of the width of an axes object.
    • h: int or float
      Expansion ratio of the width of an axes object.

    Returns

    patchworlib.Bricks object

Brick class

Subclass of matplotlib.axes.Axes object. A patchworklib.Brick object can be joined with another patchworklib.Brick(s) object using /, |, +, and - operators.

Parameters

  • bricks_dict: dict
    Dictionaly of patchworklib.Brick(s) objects. The label name of the Brick object is served as the dictionaly keys.
  • label: str
    Unique identifier for the Bricks class object. The value can be used in layout adjustment using label indexing. The value would be assigned to self.label.

Attributes

  • case: matplotlib.Axes.axes
    An invisible axes object surrounding Bricks object excluding common label, legend.
  • outline: patchworklib.Bricks
    A bricks object based on the invisible axes object surrounding all objects in the original Bricks object including case axes.
  • label: str
    Unique identifier of the Brick class object. If the Brick object is incorporated in the other super Bricks objects, the Brick object can be accessed from the super Bricks object by specifying the label name for the super object as Bricks_object[{label}].
  • bricks_dict: dict
    Dictionary with labels of the Brick object as a dictionary key and the corresponding Brick object as a dictionary value.

Methods

  • set_index(self, index, x=None, y=None, **args)

    This function is the wrapper function of self.case.text. Set a index label on 'upper left' of the Bricks object. An index labels can be added, such as those on sub-figures published in scientific journals.

    Parameters

    • index: str
      index value
    • x: float
      By default, the value will be adjusted as index label is placed on 'upper left' of the Bricks object.
    • y: flaot
      By default, the value will be adjusted as index label is placed on 'upper left' of the Bricks object.
    • args: dict
      Text properties control the appearance of the label.

    Returns

    matplotlib.text.Text object

  • set_text(self, x, y, text, **args)

  • add_colorbar(self, cmap=None, x=None, y=None, vmin=0, vmax=1, hratio=None, wratio=None, coordinate='relative', **args)

    Set a colorbar for the Brick object and return a new Bricks object including the colorbar.

    Parameters

    • cmap: Colormap, default: 'viridis'
      The colormap to use.
    • x: float, default: None
      if args['orientation'] is 'vertical', the value will be adjusted as the colorbar is placed on 'lower right' of the Bricks object. if args['orientation'] is 'horizontal', the value will be adjusted as the colorbar is placed on 'lower center' of the Bricks object. The zero position for x is the most left axes of the Brick objects in the Bricks object.
    • y: float, default: None
      if args['orientation'] is 'vertical', the value will be adjusted as the colorbar is placed on 'lower right' of the Bricks object. if args['orientation'] is 'horizontal', the value will be adjusted as the colorbar is placed on 'lower center' of the Bricks object. The zero position for y is the most bottom axes of the Brick objects in the Bricks object.
    • vmin: float, default: 0
      Minimum value to anchor the colormap.
    • vmax: float, default: 1
      Maximum value to anchor the colormap.
    • hratio: float
      Height ratio of colorbar to height of self.case.
    • wratio: float
      Width ratio of colorbar to width of self.case.
    • coordinate: str ("relative" or "absolute"), default "relative"
      If "absolute", the values of x and y will mean the inches of the distances from the base zero positions. if "relative", the values of x and y will mean the relative distances based on width and height of Bricks object from the base zero positions.

    Returns

    patchworklib.Bricks object

  • move_legend(self, new_loc, **kws)

    Move legend

    Parameters

    • new_lock: str or int
      Location argument, as in matplotlib.axes.Axes.legend().
    • kws: dict
      Other keyword arguments can be used in matplotlib.axes.Axes.legend().

    Returns

    None

  • get_inner_corner(self, labels=None)

    Return the most left, right, bottom, and top positions of the Brick objects.

    Returns

    tuple (left, right, bottom, top)

  • get_middle_corner(self, labels=None)

    Return the left, right, bottom, and top positions of self.case. patchworklib.Brick object provides case attribute. case is invisible matplotlib.axes.Axes object surrounding the Brick object and their artist, text objects.

    Returns

    tuple (left, right, bottom, top)

  • get_outer_corner(self)

    Return the left, right, bottom, and top positions of self.outline. A patchworklib.Brick object provides outline attribute. outline is Bricks object based on invisible matplotlib.axes.Axes object surrounding case axes, and its artist, text objects.

    Returns

    tuple (left, right, bottom, top)

Bricks class

A patchworklib.Bricks class object is a collection of patchworklib.Brick object. It can be joined with aother patchworklib.Brick(s) object by using /, |, -, and + operators.

Parameters

  • bricks_dict: dict
    Dictionaly of patchworklib.Brick class objects. The label name of each Brick object is served as the dictionaly keys.
  • label: str
    Unique identifier for the Bricks class object. The value can be used in layout adjustment using label indexing. The value would be assigned to self.label.

Attributes

  • case: matplotlib.Axes.axes
    Invisible axes object surrounding Bricks object excluding common label, legend.
  • outline: patchworklib.Bricks
    A patchworklib.Bricks object based on the invisible axes object surrounding all objects in the original Bricks object including case axes.
  • label: str
    Unique identifier of the Bricks class object. If the Bricks object is incorporated in the other super Bricks objects, by specifying the label name for the super object as Bricks_object[{label}], the Bricks object can be accessed from the super Bricks object.
  • bricks_dict: dict
    Dictionary with labels of the patchworklib.Brick(s) objects in the Bricks object as dictionary keys and the corresponding patchworklib.Brick(s) objects as dictionary values.

Methods

  • set_supxlabel(self, xlabel, labelpad=None, *, loc=None, **args)

    This function is the wrapper of self.case.set_xlabel. Set a common xlabel for the Bricks objects. If a Bricks class object is composed of multiple Brick(s) class objects and each has same xaxis labels, you can remove the redundant labels and can add the common x axis label for all Brick(s) objects.

    Parameters

    • xlabel: str
      xlabel value
    • labelpad: int, default: 8
      Spacing in points from the virtual axes bounding box of the Bricks object.
    • args: dict
      Text properties control the appearance of the label.

    Returns

    matplotlib.text.Text object

  • set_supylabel(self, ylabel, labelpad=None, *, loc=None, **args)

    This function is the wrapper of self.case.set_ylabel. Set a common ylabel for the Bricks objects. If a Bricks class object is composed of multiple Brick(s) class objects and each has same yaxis labels, you can remove the redundant labels and can add the common y axis label for all Brick(s) objects.

    Parameters

    • ylabel: str
      ylabel value
    • labelpad: int, default: 8
      Spacing in points from the virtual axes bounding box of the Bricks object.
    • args: dict
      Text properties control the appearance of the label.

    Returns

    matplotlib.text.Text object

  • set_suptitle(self, title, loc=None, pad=None, **args)

    This function is the wrapper of self.case.set_title. Set a common title for the Brick(s) objects. If a Bricks class object is composed of multiple Brick(s) class objects and each has common title, you can set common title for all Brick(s) objects.

    Parameters

    • title: str
      title value
    • loc: str ("center", "left", "right"), default "center" Which title to set.
    • pad: int, default: 12
      Spacing in points from the virtual axes bounding box of the Bricks object.
    • args: dict
      Text properties control the appearance of the label.

    Returns

    matplotlib.text.Text object

  • set_index(self, index, x=None, y=None, **args)

    This function is the wrapper function of self.case.text. Set a index label on 'upper left' of the Bricks object. An index labels can be added, such as those on sub-figures published in scientific journals.

    Parameters

    • index: str
      index value
    • x: float
      By default, the value will be adjusted as index label is placed on 'upper left' of the Bricks object.
    • y: flaot
      By default, the value will be adjusted as index label is placed on 'upper left' of the Bricks object.
    • args: dict
      Text properties control the appearance of the label.

    Returns

    matplotlib.text.Text object

  • set_text(self, x, y, text, **args)

  • set_supspine(self, which='left', visible=True, position=None, bounds=None)

    Set a common spine for the Bric(s) objects in the Bricks object.
    The spines of self.case surrounding the Bricks object are invisible by default. However, by applying this methods, a specified spine will be visible.

    Parameters

    Returns

    matplotlib.spines.Spine object

  • align_xlabels(self, keys=None)

    Align the xlabels of the specified Brick objects.

    Parameters

    • keys: list of str or Brick object The xlabels of the Brick objects specified by keys will be aligned.

  • align_ylabels(self, keys=None)

    Align the ylabels of the specified Brick objects.

    Parameters

    • keys: list of str or Brick object The ylabels of the Brick objects specified by keys will be aligned.

  • add_colorbar(self, cmap=None, x=None, y=None, vmin=0, vmax=1, hratio=None, wratio=None, coordinate='relative', **args)

    Set a common colorbar for the Bricks objects and return a new Bricks object including the colorbar.

    Parameters

    • cmap: Colormap, default: 'viridis' The colormap to use.
    • x: float, default: None
      if args['orientation'] is 'vertical', the value will be adjusted as the colorbar is placed on 'lower right' of the Bricks object. if args['orientation'] is 'horizontal', the value will be adjusted as the colorbar is placed on 'lower center' of the Bricks object. The zero position for x is the most left axes of the Brick objects in the Bricks object.
    • y: float, default: None
      if args['orientation'] is 'vertical', the value will be adjusted as the colorbar is placed on 'lower right' of the Bricks object. if args['orientation'] is 'horizontal', the value will be adjusted as the colorbar is placed on 'lower center' of the Bricks object. The zero position for y is the most bottom axes of the Brick objects in the Bricks object.
    • vmin: float, default: 0
      Minimum value to anchor the colormap.
    • vmax: float, default: 1
      Maximum value to anchor the colormap.
    • hratio: float
      Height ratio of colorbar to height of self.case
    • wratio: float
      Width ratio of colorbar to width of self.case
    • coordinate: str ("relative", "absolute"), default: "relative"
      if "absolute", the values of x and y will mean the inches of the distances from the base zero positions. if "relative", the values of x and y will mean the relative distances based on width and height of Bricks object from the base zero positions.

    Returns

    patchworklib.Bricks object

  • move_legend(self, new_loc, **kws)

    Move legend.

    Parameters

    • new_lock: str or int
      Location argument, as in matplotlib.axes.Axes.legend().
    • kws: dict
      Other keyword arguments can be used in matplotlib.axes.Axes.legend().

    Returns

    None

  • get_inner_corner(self)

    Return the the left, right, bottom, and top positions . The inner corners of the Bricks object means the most top left, top right, bottom left, and bottom right corners of the spines of Brick objects in the Bricks object.

    Returns

    tuple (left, right, bottom, top)

  • get_middle_corner(self)

    Return the left, right, bottom, and top positions of self.case. A patchworklib.Bricks object provides case attribute. A case is invisible matplotlib.axes.Axes object surrounding Brick objects in the Bricks object and their artist, text objects.

    Returns

    tuple (left, right, bottom, top)

  • get_outer_corner(self)

    Return the left, right, bottom, and top positions of self.outline. A patchworklib.Bricks object has outline attribute. It is a Bricks object based on invisible matplotlib.axes.Axes object surrounding case axes, and its artist, text objects.

    Returns

    tuple (left, right, bottom, top)