fraunhofer-izi / multi_bary_plot

Plot in generalized barycentric coordinates

Multi Bary Plot

A classy way to get a 2-d visualization of n-dimensional data using the generalized barycentric coordinate system.

We use the closest value in barycentric coordinates to color the pixels according to the given values. For each point the dimensions are normalized to a partition of 1 and multiplied with the vertices of the coordinat system defining polygon.

Note all dimensions need to be positive for the point to lie within the polygon and at least one dimension needs to have a value other than 0 for the position to be defined.

Install

pip install git+https://github.com/fraunhofer-izi/multi_bary_plot

Example

from multi_bary_plot import GenBary
import pandas as pd

3 Dimensions

# generate data
vec = list(range(100))
pdat = pd.DataFrame({'class 1':vec,
                     'class 2':list(reversed(vec)),
                     'class 3':[50]*100,
                     'val':vec})

# plot
bp = GenBary(pdat, 'val')

fig, ax, im = bp.imshow()

fig, ax, sc = bp.scatter()

fig, ax, ll = bp.plot()

8 Dimensions

# generate data
import numpy as np
vec2 = np.pi * np.array(range(200)) / 100
pos = np.sin(vec2) + 1
ep = np.cos(vec2*8) + 1.4
pdat2 = pd.DataFrame({'class 1':pos**ep,
                      'class 2':np.roll(pos, 25)**ep,
                      'class 3':np.roll(pos, 50)**ep,
                      'class 4':np.roll(pos, 75)**ep,
                      'class 5':np.roll(pos, 100)**ep,
                      'class 6':np.roll(pos, 125)**ep,
                      'class 7':np.roll(pos, 150)**ep,
                      'class 8':np.roll(pos, 175)**ep,
                      'val':pos*100})
# plot
bp2 = GenBary(pdat2, 'val')

fig, ax, im = bp2.imshow(cmap='plasma')

fig, ax, sc = bp2.scatter(cmap='plasma', s=2)

fig, ax, ll = bp2.plot()

Further Info

help(GenBary)

Help on class GenBary in module multi_bary_plot.multi_bary_plot:

class GenBary(builtins.object)
 |  This class can turn n-dimensional data into a
 |  2-d plot with generalized barycentric coordinates.
 |  
 |  Parameters
 |  ----------
 |  data : pandas.DataFrame
 |      Coordinates in at least 3 dimensions and an optional
 |      value column.
 |  value_column : string, optional
 |      The name of the optional value column in the `data`.
 |      If no value column is given, `imshow` is not available
 |      and `scatter` does not color the points automatically.
 |  coordinate_columns : list of strings, optional
 |      The coloumns of data that contain the positional values.
 |      If None is given, all columns but the `value_column` are
 |      used as `coordinate_columns`.
 |  res : int, optional
 |      The number of pixels along one axes; defaults to 500.
 |  ticks : list of numericals, optional
 |      The ticks of the colorbar.
 |  
 |  Returns
 |  -------
 |  GenBary : instance
 |      An instance of the GenBary.
 |  
 |  Usage
 |  -----
 |  vec = list(range(100))
 |  pdat = pd.DataFrame({'class 1':vec,
 |                       'class 2':list(reversed(vec)),
 |                       'class 3':[50]*100,
 |                       'val':vec})
 |  bp = GenBary(pdat, 'val')
 |  fig, ax, im = bp.plot()
 |  
 |  Methods defined here:
 |  
 |  __init__(self, data, value_column=None, coordinate_columns=None, res=500, ticks=None)
 |      Initialize self.  See help(type(self)) for accurate signature.
 |  
 |  draw_polygon(self, ax=None)
 |      Draws the axes and lables of the coordinate system.
 |  
 |  imshow(self, colorbar=True, fig=None, ax=None, **kwargs)
 |      Plots the data in barycentric coordinates and colors pixels
 |      according to the closest given value.
 |      
 |      Parameters
 |      ----------
 |      colorbar : bool, optional
 |          If true a colorbar is plotted on the bottom of the image.
 |          Ignored if figure is None and axes is not None.
 |      fig : matplotlib.figure, optional
 |          The figure to plot in.
 |      ax : matplotlib.axes, optional
 |          The axes to plot in.
 |      **kwargs
 |          Other keyword arguments are passed on to
 |          matplotlib.pyplot.imshow.
 |      
 |      Returns
 |      -------
 |      fig, ax, im
 |          The matplotlib Figure, AxesSubplot,
 |          and AxesImage of the plot.
 |  
 |  plot(self, fig=None, ax=None, **kwargs)
 |      Plots the data in barycentric coordinates.
 |      
 |      Parameters
 |      ----------
 |      fig : matplotlib.figure, optional
 |          The figure to plot in.
 |      ax : matplotlib.axes, optional
 |          The axes to plot in.
 |      **kwargs
 |          Other keyword arguments are passed on to
 |          matplotlib.pyplot.plot.
 |      
 |      Returns
 |      -------
 |      fig, ax, ll
 |          The matplotlib Figure, AxesSubplot,
 |          and list of Line2D of the plot.
 |  
 |  scatter(self, color=None, colorbar=None, fig=None, ax=None, **kwargs)
 |      Scatterplot of the data in barycentric coordinates.
 |      
 |      Parameters
 |      ----------
 |      color : bool, optional
 |          Color points by given values. Ignored if no value column
 |          is given.
 |      colorbar : bool, optional
 |          If true a colorbar is plotted on the bottom of the image.
 |          Ignored if figure is None and axes is not None.
 |      fige : matplotlib.figure, optional
 |          The figure to plot in.
 |      ax : matplotlib.axes, optional
 |          The axes to plot in.
 |      **kwargs
 |          Other keyword arguments are passed on to
 |          matplotlib.pyplot.scatter. The keyword argument c
 |          overwrites given values in the data.
 |      
 |      Returns
 |      -------
 |      fig, ax, pc
 |          The matplotib Figure, AxesSubplot,
 |          and PathCollection of the plot.
 |  
 |  ----------------------------------------------------------------------
 |  Data descriptors defined here:
 |  
 |  __dict__
 |      dictionary for instance variables (if defined)
 |  
 |  __weakref__
 |      list of weak references to the object (if defined)
 |  
 |  grid
 |      The grid of pixels to raster in imshow.
 |  
 |  hull
 |      The edges of the confex hull for plotting.
 |  
 |  in_hull
 |      A mask of the grid for the part outside
 |      the simplex.
 |  
 |  mgrid
 |      Melted x and y coordinates of the pixel grid.
 |  
 |  plot_values
 |      The Pixel colors masked to the inside of
 |      the barycentric coordinate system.
 |  
 |  points_2d
 |      The 2-d coordinates of the given points.
 |  
 |  text_position
 |      Dimensions label positions in plot.
 |  
 |  vertices
 |      The vertices of the barycentric coordinate system.