Re: [Rdkit-discuss] Interactive plots in Jupyter notebooks (Chris Swain)

2020-01-16 Thread Chris Swain via Rdkit-discuss 
Hi,

Thanks for all the suggestions, both on and off list, it is clear that this is 
of considerable interest. Several people have asked me to post details.

I’ve tried to summarise my findings, bear in mind this is a work in progress! 
(There is also a download link to the notebook and the datafile)

https://www.macinchem.org/reviews/fdamols/interactiveplots.php 


I’ve also put up a Jupyter notebook with examples of the different options 
here, 

https://www.macinchem.org/reviews/fdamols/interaction.html 


If anyone has other suggestions I’d be interested to hear about them.

Cheers,

Chris

> 
> On 15 Jan 2020, at 10.30, Chris Swain via Rdkit-discuss 
> mailto:rdkit-discuss@lists.sourceforge.net>>
>  wrote:
> 
> Hi,
> 
> I've been looking at ways to produce interactive plots within a Jupyter 
> notebook and after trying a couple of options I used Plotly. This seems 
> fairly straight-forward to use and I can produce interactive data frames, in 
> addition to 2D and 3D scatterplots.
> 
> https://www.macinchem.org/blog/files/a5cc1afff58a411056af7b8d9b0011dd-2577.php
> 
> Whilst I can get text to appear when hovering over a data point I'd be 
> interested in ideas of how to get the structure displayed when you mouse over 
> a point.
> 
> Cheers,
> 
> Chris
> 
> 
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Re: [Rdkit-discuss] Interactive plots in Jupyter notebooks

2020-01-15 Thread Jan Halborg Jensen 
Hi Chris

Iwatobipen had this example using d3js 
https://iwatobipen.wordpress.com/2019/01/19/plot-chemical-space-with-d3js-based-library-rdkit-chemoinformatics/

I made a simple version here 
https://colab.research.google.com/drive/11rmBtA6nBgJIp_V_i_tafvffE5ZdY5Uz

https://youtu.be/ORKOoLHc-Xg

Best regards, Jan

On 15 Jan 2020, at 10.30, Chris Swain via Rdkit-discuss 
mailto:rdkit-discuss@lists.sourceforge.net>>
 wrote:

Hi,

I've been looking at ways to produce interactive plots within a Jupyter 
notebook and after trying a couple of options I used Plotly. This seems fairly 
straight-forward to use and I can produce interactive data frames, in addition 
to 2D and 3D scatterplots.

https://www.macinchem.org/blog/files/a5cc1afff58a411056af7b8d9b0011dd-2577.php

Whilst I can get text to appear when hovering over a data point I'd be 
interested in ideas of how to get the structure displayed when you mouse over a 
point.

Cheers,

Chris


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Re: [Rdkit-discuss] Interactive plots in Jupyter notebooks

2020-01-15 Thread Jennifer Hemmerich 

Hi Chris,

I remember that a colleague of mine once used images of the molecules 
for that. However he did it in R and so far I also have not really 
succeeded to redo this as his code is not available anymore (but did 
also not try too hard).


If images are an option you can look here, it requires some workarounds 
but might be an option: 
https://github.com/etpinard/plotly-dashboards/tree/master/hover-images


In any case if you find a possibility I would be really interested if 
you would be willing to share =)


Best,

Jennifer

On 15.01.20 11:12, Axel Pahl wrote:

Hi Chris,

i too, looked for this functionality in Plotly, but I was not able to 
find it.

This is the reason I switched to bokeh / holoviews.

https://github.com/apahl/mol_frame/blob/68801e16af3cfb60f846c40f471d190cbe34748b/mol_frame/mol_frame.py#L949 
and

https://github.com/apahl/mol_frame/blob/68801e16af3cfb60f846c40f471d190cbe34748b/mol_frame/mol_frame.py#L1214

Kind regards,
Axel

On 15.01.20 10:30, Chris Swain via Rdkit-discuss wrote:

Hi,

I've been looking at ways to produce interactive plots within a 
Jupyter notebook and after trying a couple of options I used Plotly. 
This seems fairly straight-forward to use and I can produce 
interactive data frames, in addition to 2D and 3D scatterplots.


https://www.macinchem.org/blog/files/a5cc1afff58a411056af7b8d9b0011dd-2577.php

Whilst I can get text to appear when hovering over a data point I'd 
be interested in ideas of how to get the structure displayed when you 
mouse over a point.


Cheers,

Chris




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Re: [Rdkit-discuss] Interactive plots in Jupyter notebooks

2020-01-15 Thread Axel Pahl 

Hi Chris,

i too, looked for this functionality in Plotly, but I was not able to
find it.
This is the reason I switched to bokeh / holoviews.

https://github.com/apahl/mol_frame/blob/68801e16af3cfb60f846c40f471d190cbe34748b/mol_frame/mol_frame.py#L949
and
https://github.com/apahl/mol_frame/blob/68801e16af3cfb60f846c40f471d190cbe34748b/mol_frame/mol_frame.py#L1214

Kind regards,
Axel

On 15.01.20 10:30, Chris Swain via Rdkit-discuss wrote:

Hi,

I've been looking at ways to produce interactive plots within a
Jupyter notebook and after trying a couple of options I used Plotly.
This seems fairly straight-forward to use and I can produce
interactive data frames, in addition to 2D and 3D scatterplots.

https://www.macinchem.org/blog/files/a5cc1afff58a411056af7b8d9b0011dd-2577.php

Whilst I can get text to appear when hovering over a data point I'd be
interested in ideas of how to get the structure displayed when you
mouse over a point.

Cheers,

Chris




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