molplotly 0.13

molplotly is an add-on to plotly built on RDKit which allows 2D images of molecules to be shown in scatterplots when hovering over the datapoints.

molplotly

molplotly is an add-on to plotly built on RDKit which allows 2D images of molecules to be shown in scatterplots when hovering over the datapoints.

Required packages:

• rdkit
• pandas
• jupyter_dash

➡️ See example.ipynb for an example :)

📜 Usage

import pandas as pd
import plotly.express as px

import molplotly

# load a DataFrame with smiles
df_esol = pd.read_csv('esol.csv')
df_esol['y_pred'] = df_esol['ESOL predicted log solubility in mols per litre']
df_esol['y_true'] = df_esol['measured log solubility in mols per litre']

# generate a scatter plot
fig = px.scatter(df_esol, x="y_true", y="y_pred")

# add molecules to the plotly graph - returns a Dash app
app = molplotly.add_molecules(fig=fig, 
                            df=df_esol, 
                            smiles_col='smiles', 
                            title_col='Compound ID', 
                            )

# run Dash app inline in notebook (or in an external server)
app.run_server(mode='inline', port=8011, height=1000)

Input parameters

• fig : plotly.graph_objects.Figure object
  a plotly figure object containing datapoints plotted from df
• df : pandas.DataFrame object
  a pandas dataframe that contains the data plotted in fig
• smiles_col : str, optional
  name of the column in df containing the smiles plotted in fig (default 'SMILES')
• show_img : bool, optional
  whether or not to generate the molecule image in the dash app (default True)
• title_col : str, optional
  name of the column in df to be used as the title entry in the hover box (default None)
• show_coords : bool, optional
  whether or not to show the coordinates of the data point in the hover box (default True)
• caption_cols : list, optional
  list of column names in df to be included in the hover box (default None)
• condition_col : str, optional
  name of the column in df that is used to color the datapoints in df - necessary when there is discrete conditional coloring (default None)
• wrap : bool, optional
  whether or not to wrap the title text to multiple lines if the length of the text is too long (default True)
• wraplen : int, optional
  the threshold length of the title text before wrapping begins - adjust when changing the width of the hover box (default 20)
• width : int, optional
  the width in pixels of the hover box (default 150)
• fontfamily : str, optional
  the font family used in the hover box (default 'Arial')
• fontsize : int, optional
  the font size used in the hover box - the font of the title line is fontsize+2 (default 12)

Output parameters

by default a JupyterDash app is returned which can be run inline in a jupyter notebook or deployed on a server via app.run_server()

Acknowledgements

• @wjm41 (contributor)
• @RokasEl (contributor)

Features to-add:

1. Individual styles for each caption (fonts, colors etc)
2. Some way to save the plot
3. Highlight points by clicking on them
4. SVG image generation