arosen93 / ptable_trends

Periodic Trend Plotter

Python script to plot periodic trends as a heat map over the periodic table of elements.

Usage

This Python script (ptable_trends.py) can be used to plot a heat map over an image of the periodic table of elements for easy and automated visualization of periodic trends.

A minimal example is as follows:

from ptable_trends import ptable_plotter
ptable_plotter("ionization_energies.csv")

The only required argument to ptable_plotter() is a single positional argument for the full filepath/name (with extension) of the data file containing your periodic trend data. The data file must be in a comma-separated value (.csv) format with the first entry in each row being the atom symbol and the second entry being the value you wish to plot. An example .csv file is included in this repository for testing purposes under the name ionization_energies.csv. After the ptable_trends.py script is run, it will show the plot in your web browser. To save the image, simply click the save icon that appears in the web browser figure.

There are numerous optional arguments, which can be used to modify the appearance of the figure. The full argument list is below:

ptable_trends/ptable_trends.py

Lines 20 to 93 in 529d23e

    
           def ptable_plotter( 
        
               filename: str, 
        
               show: bool = True, 
        
               output_filename: str = None, 
        
               width: int = 1050, 
        
               cmap: str = "plasma", 
        
               alpha: float = 0.65, 
        
               extended: bool = True, 
        
               periods_remove: List[int] = None, 
        
               groups_remove: List[int] = None, 
        
               log_scale: bool = False, 
        
               cbar_height: float = None, 
        
               cbar_standoff: int = 12, 
        
               cbar_fontsize: int = 14, 
        
               blank_color: str = "#c4c4c4", 
        
               under_value: float = None, 
        
               under_color: str = "#140F0E", 
        
               over_value: float = None, 
        
               over_color: str = "#140F0E", 
        
               special_elements: List[str] = None, 
        
               special_color: str = "#6F3023", 
        
           ) -> figure: 
        
               """ 
        
               Plot a heatmap over the periodic table of elements. 
        
               Parameters 
        
               ---------- 
        
               filename : str 
        
                   Path to the .csv file containing the data to be plotted. 
        
               show : str 
        
                   If True, the plot will be shown. 
        
               output_filename : str 
        
                   If not None, the plot will be saved to the specified (.html) file. 
        
               width : float 
        
                   Width of the plot. 
        
               cmap : str 
        
                   plasma, infnerno, viridis, or magma 
        
               alpha : float 
        
                   Alpha value (transparency). 
        
               extended : bool 
        
                   If True, the lanthanoids and actinoids will be shown. 
        
               periods_remove : List[int] 
        
                   Period numbers to be removed from the plot. 
        
               groups_remove : List[int] 
        
                   Group numbers to be removed from the plot. 
        
               log_scale : bool 
        
                   If True, the colorbar will be logarithmic. 
        
               cbar_height : int 
        
                   Height of the colorbar. 
        
               cbar_standoff : int 
        
                   Distance between the colorbar and the plot. 
        
               cbar_fontsize : int 
        
                   Fontsize of the colorbar label. 
        
               blank_color : str 
        
                   Hexadecimal color of the elements without data. 
        
               under_value : float 
        
                   Values <= under_value will be colored with under_color. 
        
               under_color : str 
        
                   Hexadecimal color to be used for the lower bound color. 
        
               over_value : float 
        
                   Values >= over_value will be colored with over_color. 
        
               under_color : str 
        
                   Hexadecial color to be used for the upper bound color. 
        
               special_elements: List[str] 
        
                   List of elements to be colored with special_color. 
        
               special_color: str 
        
                   Hexadecimal color to be used for the special elements. 
        
               Returns 
        
               ------- 
        
               figure 
        
                   Bokeh figure object. 
        
               """

A couple of examples using various optional keyword arguments are as follows:

from ptable_trends import ptable_plotter
ptable_plotter("ionization_energies.csv", log_scale=True)

from ptable_trends import ptable_plotter
ptable_plotter("ionization_energies.csv", cmap="viridis", alpha=0.7, extended=False, periods_remove=[1])

Dependencies

The script requires the following dependencies:

These packages can be installed using pip via pip install -r requirements.txt in the ptable_trends base directory.

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arosen93 / ptable_trends

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Periodic Trend Plotter

Usage

Dependencies

	def ptable_plotter(
	filename: str,
	show: bool = True,
	output_filename: str = None,
	width: int = 1050,
	cmap: str = "plasma",
	alpha: float = 0.65,
	extended: bool = True,
	periods_remove: List[int] = None,
	groups_remove: List[int] = None,
	log_scale: bool = False,
	cbar_height: float = None,
	cbar_standoff: int = 12,
	cbar_fontsize: int = 14,
	blank_color: str = "#c4c4c4",
	under_value: float = None,
	under_color: str = "#140F0E",
	over_value: float = None,
	over_color: str = "#140F0E",
	special_elements: List[str] = None,
	special_color: str = "#6F3023",
	) -> figure:

	"""
	Plot a heatmap over the periodic table of elements.

	Parameters
	----------
	filename : str
	Path to the .csv file containing the data to be plotted.
	show : str
	If True, the plot will be shown.
	output_filename : str
	If not None, the plot will be saved to the specified (.html) file.
	width : float
	Width of the plot.
	cmap : str
	plasma, infnerno, viridis, or magma
	alpha : float
	Alpha value (transparency).
	extended : bool
	If True, the lanthanoids and actinoids will be shown.
	periods_remove : List[int]
	Period numbers to be removed from the plot.
	groups_remove : List[int]
	Group numbers to be removed from the plot.
	log_scale : bool
	If True, the colorbar will be logarithmic.
	cbar_height : int
	Height of the colorbar.
	cbar_standoff : int
	Distance between the colorbar and the plot.
	cbar_fontsize : int
	Fontsize of the colorbar label.
	blank_color : str
	Hexadecimal color of the elements without data.
	under_value : float
	Values <= under_value will be colored with under_color.
	under_color : str
	Hexadecimal color to be used for the lower bound color.
	over_value : float
	Values >= over_value will be colored with over_color.
	under_color : str
	Hexadecial color to be used for the upper bound color.
	special_elements: List[str]
	List of elements to be colored with special_color.
	special_color: str
	Hexadecimal color to be used for the special elements.

	Returns
	-------
	figure
	Bokeh figure object.
	"""