matplotlib sharex with colorbar not working

Question

I have 2 subplots- 1 scatter and one bar for which I would like a shared x axis. The scatter plot has a color bar. The sharex doesn't seem to work with this as the axis for the two plots do not coincide. My code:

fig, (ax, ax2) = plt.subplots(2,1, gridspec_kw = {'height_ratios':[13,2]},figsize=(15,12), sharex=True)

df_plotdata.plot(kind='scatter', ax=ax, x='index_cancer', y='index_g', s=df_plotdata['freq1']*50, c=df_plotdata['freq2'], cmap=cmap)

df2.plot(ax=ax2, x='index_cancer', y='freq', kind = 'bar')

Answer 1

Sharex means that the axes limits are the same and that the axes are synchronized. It doesn't mean that they lie on top of each other. It all depends on how you create the colorbar.

The colorbar created by pandas scatterplot is, just like any statndard colorbar in matplotlib, created by taking away part of the space for the axes that it relates to. Hence this axes is smaller than other axes from the grid.

Options you have include:

• Shrinking the other axes of the grid by the same amount than the scatterplot axes.
  This can be done by using the position of the first axes and set the position of the second axes accordingly, using ax.get_position() and ax.set_postion()

  import matplotlib.pyplot as plt
  import pandas as pd
  import numpy as np
  import itertools as it
  
  xy = list( it.product( range(10), range(10) ) )
  df = pd.DataFrame( xy, columns=['x','y'] )
  df['score'] = np.random.random( 100 )
  
  kw = {'height_ratios':[13,2]}
  fig, (ax,ax2) = plt.subplots(2,1,  gridspec_kw=kw, sharex=True)
  
  df.plot(kind='scatter', x='x',  y='y', c='score', s=100, cmap="PuRd",
            ax=ax, colorbar=True)
  df.groupby("x").mean().plot(kind = 'bar', y='score',ax=ax2, legend=False)
  
  ax2.legend(bbox_to_anchor=(1.03,0),loc=3)
  
  pos = ax.get_position()
  pos2 = ax2.get_position()
  ax2.set_position([pos.x0,pos2.y0,pos.width,pos2.height])
  
  plt.show()
  

• Create a grid including an axes for the colorbar.
  In this case you can create a 4 by 4 grid and add the colorbar to the upper right axes of it. This requires to supply the scatter plot to fig.colorbar() and specify an axes for the colorbar to live in,

  fig.colorbar(ax.collections[0], cax=cax)       
  

  Then remove the lower right axes, which is not needed (ax.axis("off")). You may still share the axes, if that is needed, via ax2.get_shared_x_axes().join(ax, ax2).

  import matplotlib.pyplot as plt
  import pandas as pd
  import numpy as np
  import itertools as it
  
  
  xy = list( it.product( range(10), range(10) ) )
  df = pd.DataFrame( xy, columns=['x','y'] )
  df['score'] = np.random.random( 100 )
  
  kw = {'height_ratios':[13,2], "width_ratios":[95,5]}
  fig, ((ax, cax),(ax2,aux)) = plt.subplots(2,2,  gridspec_kw=kw)
  
  df.plot(kind='scatter', x='x',  y='y', c='score', s=80, cmap="PuRd",
           ax=ax,colorbar=False)
  df.groupby("x").mean().plot(kind = 'bar', y='score',ax=ax2, legend=False)
  
  fig.colorbar(ax.collections[0], cax=cax, label="score")
  aux.axis("off")
  ax2.legend(bbox_to_anchor=(1.03,0),loc=3)
  ax2.get_shared_x_axes().join(ax, ax2)
  ax.tick_params(axis="x", labelbottom=0)
  ax.set_xlabel("")
  
  plt.show()
  

Answer 2

Based on ImportanceOfBeingErnest's answer the two following functions would align the axis:

def align_axis_x(ax, ax_target):
    """Make x-axis of `ax` aligned with `ax_target` in figure"""
    posn_old, posn_target = ax.get_position(), ax_target.get_position()
    ax.set_position([posn_target.x0, posn_old.y0, posn_target.width, posn_old.height])

def align_axis_y(ax, ax_target):
    """Make y-axis of `ax` aligned with `ax_target` in figure"""
    posn_old, posn_target = ax.get_position(), ax_target.get_position()
    ax.set_position([posn_old.x0, posn_target.y0, posn_old.width, posn_target.height])