Python plotting cheatsheet

Bookmarks

• Python graph gallery
• Seaborn
• Matplotlib
  • Examples - has a lot of examples
  • Userguide
  • Matplotlib Colors

To try out

• pygwalker
• Bokeh
• ggplot

Matplotlib

Figure layout

• use subfigures + subfigures to make publication level figures in one shot

  fig = plt.figure(layout='constrained', figsize=(10, 4))
  subfigs = fig.subfigures(nrows=1, ncols=2, 
  						 wspace=0.07, hspace=None,
  						 width_ratios=[1.5,1], 
  						 height_ratios=None)
   
   
  axsL = subfigs[0].subplots(nrows=1, ncols=2, 
  						   sharex=False, sharey=True)
  axsR = subfigs[1].subplots(nrows=1, ncols=2, 
  						   sharex=True, sharey=False)

• subfigures guide (doc sheet)

• subplot_mosaic for complicated axes - guide

axs = subfigs[0].subplot_mosaic(
"""
abc
""",
width_ratios=[1,0.75,1.5],
sharey=True
)
```

Figure axes

• axis labels

  ax.set_xlabel('X-axis')
  ax.set_ylabel('Y-axis')

• I prefer removing the axes and spine. despine from seaborn generally works well, but in some cases spines still remain so I switch of visibility for those

  sns.despine(ax=ax, trim=True, offset=5)

ax.spines’right’, ‘top’.set_visible(False)
```

• more axes modifications

   
  ax.spines['bottom'].set_color('red')
  ax.spines['top'].set_color('red')
  ax.xaxis.label.set_color('red')
  ax.tick_params(axis='x', colors='red')
   

• axis limits

  ax.axis([350, 700, 0, 1])
  ax.set_xlim()
  ax.xaxis.set_ticks()

Multiple x, y axis

• guide - here

• Make multiple y axis by:

  ax_r = ax.twinx()
  # use ax_r as normal

• Make multiple x axis by using ax.twiny()

Plot

the workhorse - doc sheet

ax.plot(x,y,color='tab:orange')
ax.plot(x,y, dashes=[2, 2], label='__nolabel__', color='k') #dashed line

Fill between

• Easy to make filled plots, highlight stimulus areas, etc
• demo

ax.fill_between(x, 0, y, label='label', facecolor=('color', alpha)) # has no edge line
ax.fill_between(x, 0, y, label='label', color=('#000', 0.3)) # with a line edge

Ordering artists

• Note: This does not work with twin axes

• Probably works with other types of axes, not sure

• Works with different plots. Higher zorder implies it will be on top¹

• Demo

  plot(..., zorder=10)

Labels

• Changing location orientation of x and y labels

  ax.set_ylabel('Label', rotation=270)
  ax.yaxis.set_label_coords(1.12,0.5)

Colorbars

• Colorbar tutorial

• Placing colorbars

• Colorbar tick labeling demo

• Adding an colorbar to an axes:

  cbar = fig.colorbar(mpl.cm.ScalarMappable(norm= mpl.colors.Normalize(0, 1), cmap='viridis'), ax=ax, orientation='vertical', ticks=[0, 1], format=mpl.ticker.FixedFormatter(['min', 'max']))

• Modifying cbar labels:

  cbar.set_label("Label", rotation=270)

Legends

• a very nice guide for customizing legends (doc sheet)
• use _nolegend_ to skip plots from appearing in legend²
• you can hook it to subplots or subfigures or figures.
• bbox_to_anchor coupled with loc is a good way of moving the legend to where you would like it in the plot.

example:

legend(legend_str, loc='outside upper right', frameon=False, bbox_to_anchor=(1.0, 0.96))

Text

• To add annotations to the text - guide (doc sheet)

  ax.text(x,y,'$\mu=$%d'%(text), color=text_color, 
  		weight='bold', ha=align)

Saving figures

• Typically, I save as a pdf as svg rarely works well for me with Affinity designer.
• Using bbox_inches='tight' allows legends and other modifications that go beyond 1 in a normalized fig size.³

fig.savefig("figure.pdf", bbox_inches='tight')

Footnotes

1. https://stackoverflow.com/questions/17431441/matplotlib-scatter-plot-to-foreground-on-top-of-a-contour-plot ↩

2. https://stackoverflow.com/questions/24680981/show-only-certain-items-in-legend - note, label=None did not work for me ↩

3. https://stackoverflow.com/a/71663610 ↩