Tweak plots - Githubissues

bas-rustenburg commented 7 years ago

Based on some preferences, plotting functions were updated.

What:

The charge/tautomer heatmap has been updated to shade tautomers of the same charge, instead of shading based on just the state index alone.
Lightness of tautomer shading has been updated.

Also, here is an example script, which updates labels among other things specific to the Abl:Imatinib application.

from netCDF4 import Dataset
from protons.app import analysis
from matplotlib import pyplot as plt
ds = Dataset("Abl-Imatinib-full.nc", mode='r')
ylabels = (ds['Protons/Metadata/residue_name'][:])
for i,y in enumerate(ylabels):
   # leave out first 16 characters, which contain "Chain X Residue"
    ylabels[i] = y[16:]

x = analysis.plot_tautomer_heatmap(ds)
# Label by residue name
plt.yticks(list(y -0.5 for y  in range(1,len(ylabels)+1)), ylabels, size='small', rotation=0)
plt.xticks(range(25,231,25), list(x *0.020 for x in range(25,231,25)), size='small', rotation=0)
plt.xlabel("Time (ns)")
plt.title("Abl:Imatinib residue charge (color) and tautomers (shade)")
plt.gca().invert_yaxis() # lowest residue number at the top. 
plt.show()

Example plot: tautomers_abl_residues_projectors.pdf