Visualizations

Various functions are provided to visualize information about a plate, a recipe, or a recipe step.

Plates

Substances

get_substance returns the set of all get_substances in a plate.

>>> plate.get_substance()
{<Substance: salt>, <Substance: water>}

Amounts

get_moles returns a numpy array of the amount of each substance in a plate.

>>> plate.get_moles(substance=salt, unit='umol')
array([[20., 20., 20., 20., 20., 20., 20., 20., 20., 20., 20., 20.],
       [10., 10., 10., 10., 10., 10., 10., 10., 10., 10., 10., 10.],
       [10., 10., 10., 10., 10., 10., 10., 10., 10., 10., 10., 10.],
       [10., 10., 10., 10., 10., 10., 10., 10., 10., 10., 10., 10.],
       [10., 10., 10., 10., 10., 10., 10., 10., 10., 10., 10., 10.],
       [10., 10., 10., 10., 10., 10., 10., 10., 10., 10., 10., 10.],
       [10., 10., 10., 10., 10., 10., 10., 10., 10., 10., 10., 10.],
       [10., 10., 10., 10., 10., 10., 10., 10., 10., 10., 10., 10.]])

get_volumes returns a numpy array of the volume of each or all substances in a plate.

>>> plate.get_volumes(substance=salt, unit='uL')
array([[1.2, 1.2, 1.2, 1.2, 1.2, 1.2, 1.2, 1.2, 1.2, 1.2, 1.2, 1.2],
       [0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6],
       [0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6],
       [0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6],
       [0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6],
       [0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6],
       [0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6],
       [0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6]])

>>> plate.get_volumes(unit='uL')
array([[10.6, 10.6, 10.6, 10.6, 10.6, 10.6, 10.6, 10.6, 10.6, 10.6, 10.6, 10.6],
       [10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. ],
       [10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. ],
       [10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. ],
       [10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. ],
       [10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. ],
       [10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. ],
       [10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. , 10. ]])

Dataframes

dataframe returns a styled pandas dataframe of the amount of each or all substance in a plate.

• By default the data is returned for all substances. A specific substance can be specified.

• You can specify what data you are interested in by passing the unit argument.

  • If you want the amount of moles of each substance in a plate, you can pass unit=’umol’.

  • If you want the volume of each substance in a plate, you can pass unit=’uL’.

  • If you want the mass of each substance in a plate, you can pass unit=’mg’.

  • If you want the concentration of each well in a plate with respect to a substance, you can pass unit=’M’. - In this case, a substance must be specified. - Any valid concentration unit can be used.

>>> plate.dataframe(substance=salt, unit='umol')

>>> plate.dataframe(unit='uL')

>>> plate.dataframe(substance=salt, unit='mg')

>>> plate.dataframe(substance=salt, unit='M')

Slices

All of the above functions can be applied to a slice of a plate.

>>> plate[:2, :2].get_volumes(unit='uL')
array([[10.6, 10.6],
       [10. , 10. ]])

>>> plate[:2, :2].dataframe(unit='uL')

Recipes

If we want to visualize what happened to a plate during part or all of a recipe, we can use the visualize method of the recipe.

• The visualize method can be used to visualize the final state of a plate or the change in a plate.

  • The mode argument can be used to specify what we are interested in.

  • ‘delta’ will show the change in the plate during the step.

  • ‘final’ will show the final state of the plate after the step.

• We can get information about certain substances or all substances in the plate.

  • ‘all’ will show information about all substances in the plate.

• We can specify the unit we are interested in. (moles, volume, or mass)

>>> recipe.visualize(what=plate, mode='final', unit='uL')

Recipe Steps

• When a recipe is baked, all the steps are stored in the steps attribute of the recipe.

• Each step has a visualize method that can be used to visualize the step, using the same arguments as the visualize method of the recipe.

>>> for i, step in enumerate(recipe.steps):
        print(f"Step: {i+1}")
        display(step)