search

MaayanLab / clustergrammer-web

Create a clustergram visualization from a user defined network in tsv format.
MIT License
11 stars 9 forks source link

format of the json input file? support for hierarchical clustering? #1

Closed paul-shannon closed 7 years ago

paul-shannon commented 8 years ago

Is there documentation for the json input files? I see row_nodes, col_nodes, links, and reverse engineering the formal structure might not be so hard. But a formal statement of the expected file structure would be very helpful.

For what it's worth, I will be generating matrices in R, sending them as JSON over websockets to the browser.

Is there any support - now, or planned - for hierarchical clustering? It -seems- (to my eye, on first look) that the clustering of rows and columns is more flat than tree-like.

Thanks for this very fine javascript widget.

cornhundred commented 8 years ago

Hi Paul,

Thanks for your interest. I'm still updating the documentation for the JSON format. Here is a link to the current documentation https://github.com/MaayanLab/clustergrammer#clustergrammer-json-format

And here is an example json - https://github.com/MaayanLab/clustergrammer/blob/master/json/mult_view.json

The format does support hierarchical clustering - each clustergram has 10 hierarchical group levels. You can encode this in the group value. Here's an interactive demo that shows how to interact with the dendrogram here http://amp.pharm.mssm.edu/clustergrammer/

You can also use the clustergrammer.py module to produce the json https://github.com/MaayanLab/clustergrammer#clustergrammer-python-module

I'll let you know when I've updated the documentation. Please let me know if you have any questions.

Best, Nick

On Fri, Jul 15, 2016 at 10:55 PM, Paul Shannon notifications@github.com wrote:

Is there documentation for the json input files? I see row_nodes, col_nodes, links, and reverse engineering the formal structure might not be so hard. But a formal statement of the expected file structure would be very helpful.

For what it's worth, I will be generating matrices in R, sending them as JSON over websockets to the browser.

Is there any support - now, or planned - for hierarchical clustering? It -seems- (to my eye, on first look) that the clustering of rows and columns is more flat than tree-like.

Thanks for this very fine javascript widget.

  • Paul

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/MaayanLab/clustergrammer-web/issues/1, or mute the thread https://github.com/notifications/unsubscribe-auth/AH90SMnAR50y-bP3dFNep5m8Gf1Pb4w3ks5qWEgQgaJpZM4JN57J .

paul-shannon commented 8 years ago

Hi Nick,

Thanks for these answers and suggestions.

Wishing to get a quick start, and deferring R for a while, I just spent some time trying to get clustergrammer.py working on rc_two_cats.txt. Discovering that your code is python 2.7, not 3.5, I hacked my way through a partial revision of your code, hoping to squeak out that quick start. I didn’t quite make it.

Maybe a >= 3.5.1 version of your package is in the works?

Now I will turn to your docs on the json format, so how that goes.

I am eager to use your heatmap. Thanks again.

On Jul 16, 2016, at 10:29 AM, Nicolas Fernandez notifications@github.com wrote:

Hi Paul,

Thanks for your interest. I'm still updating the documentation for the JSON format. Here is a link to the current documentation https://github.com/MaayanLab/clustergrammer#clustergrammer-json-format

And here is an example json - https://github.com/MaayanLab/clustergrammer/blob/master/json/mult_view.json

The format does support hierarchical clustering - each clustergram has 10 hierarchical group levels. You can encode this in the group value. Here's an interactive demo that shows how to interact with the dendrogram here http://amp.pharm.mssm.edu/clustergrammer/

You can also use the clustergrammer.py module to produce the json https://github.com/MaayanLab/clustergrammer#clustergrammer-python-module

I'll let you know when I've updated the documentation. Please let me know if you have any questions.

Best, Nick

On Fri, Jul 15, 2016 at 10:55 PM, Paul Shannon notifications@github.com wrote:

Is there documentation for the json input files? I see row_nodes, col_nodes, links, and reverse engineering the formal structure might not be so hard. But a formal statement of the expected file structure would be very helpful.

For what it's worth, I will be generating matrices in R, sending them as JSON over websockets to the browser.

Is there any support - now, or planned - for hierarchical clustering? It -seems- (to my eye, on first look) that the clustering of rows and columns is more flat than tree-like.

Thanks for this very fine javascript widget.

  • Paul

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/MaayanLab/clustergrammer-web/issues/1, or mute the thread https://github.com/notifications/unsubscribe-auth/AH90SMnAR50y-bP3dFNep5m8Gf1Pb4w3ks5qWEgQgaJpZM4JN57J .

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

paul-shannon commented 8 years ago

I installed python 2.7. Everything works great. Very nice software!

If you are so inclined, support for python > 3.5 would be useful to us here at the ISB.

On Jul 17, 2016, at 6:57 PM, Paul Shannon paul.thurmond.shannon@gmail.com wrote:

Hi Nick,

Thanks for these answers and suggestions.

Wishing to get a quick start, and deferring R for a while, I just spent some time trying to get clustergrammer.py working on rc_two_cats.txt. Discovering that your code is python 2.7, not 3.5, I hacked my way through a partial revision of your code, hoping to squeak out that quick start. I didn’t quite make it.

Maybe a >= 3.5.1 version of your package is in the works?

Now I will turn to your docs on the json format, so how that goes.

I am eager to use your heatmap. Thanks again.

  • Paul

On Jul 16, 2016, at 10:29 AM, Nicolas Fernandez notifications@github.com wrote:

Hi Paul,

Thanks for your interest. I'm still updating the documentation for the JSON format. Here is a link to the current documentation https://github.com/MaayanLab/clustergrammer#clustergrammer-json-format

And here is an example json - https://github.com/MaayanLab/clustergrammer/blob/master/json/mult_view.json

The format does support hierarchical clustering - each clustergram has 10 hierarchical group levels. You can encode this in the group value. Here's an interactive demo that shows how to interact with the dendrogram here http://amp.pharm.mssm.edu/clustergrammer/

You can also use the clustergrammer.py module to produce the json https://github.com/MaayanLab/clustergrammer#clustergrammer-python-module

I'll let you know when I've updated the documentation. Please let me know if you have any questions.

Best, Nick

On Fri, Jul 15, 2016 at 10:55 PM, Paul Shannon notifications@github.com wrote:

Is there documentation for the json input files? I see row_nodes, col_nodes, links, and reverse engineering the formal structure might not be so hard. But a formal statement of the expected file structure would be very helpful.

For what it's worth, I will be generating matrices in R, sending them as JSON over websockets to the browser.

Is there any support - now, or planned - for hierarchical clustering? It -seems- (to my eye, on first look) that the clustering of rows and columns is more flat than tree-like.

Thanks for this very fine javascript widget.

  • Paul

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/MaayanLab/clustergrammer-web/issues/1, or mute the thread https://github.com/notifications/unsubscribe-auth/AH90SMnAR50y-bP3dFNep5m8Gf1Pb4w3ks5qWEgQgaJpZM4JN57J .

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

cornhundred commented 8 years ago

Paul,

Great, I'm glad that worked out. I agree that python 3.5 support is a good idea and I'll let you know when that is available :)

Thanks for the feedback.

Best, Nick

On Jul 18, 2016 12:45 AM, "Paul Shannon" notifications@github.com wrote:

I installed python 2.7. Everything works great. Very nice software!

If you are so inclined, support for python > 3.5 would be useful to us here at the ISB.

  • Paul

On Jul 17, 2016, at 6:57 PM, Paul Shannon < paul.thurmond.shannon@gmail.com> wrote:

Hi Nick,

Thanks for these answers and suggestions.

Wishing to get a quick start, and deferring R for a while, I just spent some time trying to get clustergrammer.py working on rc_two_cats.txt. Discovering that your code is python 2.7, not 3.5, I hacked my way through a partial revision of your code, hoping to squeak out that quick start. I didn’t quite make it.

Maybe a >= 3.5.1 version of your package is in the works?

Now I will turn to your docs on the json format, so how that goes.

I am eager to use your heatmap. Thanks again.

  • Paul

On Jul 16, 2016, at 10:29 AM, Nicolas Fernandez < notifications@github.com> wrote:

Hi Paul,

Thanks for your interest. I'm still updating the documentation for the JSON format. Here is a link to the current documentation https://github.com/MaayanLab/clustergrammer#clustergrammer-json-format

And here is an example json -

https://github.com/MaayanLab/clustergrammer/blob/master/json/mult_view.json

The format does support hierarchical clustering - each clustergram has 10 hierarchical group levels. You can encode this in the group value. Here's an interactive demo that shows how to interact with the dendrogram here http://amp.pharm.mssm.edu/clustergrammer/

You can also use the clustergrammer.py module to produce the json

https://github.com/MaayanLab/clustergrammer#clustergrammer-python-module

I'll let you know when I've updated the documentation. Please let me know if you have any questions.

Best, Nick

On Fri, Jul 15, 2016 at 10:55 PM, Paul Shannon < notifications@github.com> wrote:

Is there documentation for the json input files? I see row_nodes, col_nodes, links, and reverse engineering the formal structure might not be so hard. But a formal statement of the expected file structure would be very helpful.

For what it's worth, I will be generating matrices in R, sending them as JSON over websockets to the browser.

Is there any support - now, or planned - for hierarchical clustering? It -seems- (to my eye, on first look) that the clustering of rows and columns is more flat than tree-like.

Thanks for this very fine javascript widget.

  • Paul

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/MaayanLab/clustergrammer-web/issues/1, or mute the thread < https://github.com/notifications/unsubscribe-auth/AH90SMnAR50y-bP3dFNep5m8Gf1Pb4w3ks5qWEgQgaJpZM4JN57J

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/MaayanLab/clustergrammer-web/issues/1#issuecomment-233227954, or mute the thread https://github.com/notifications/unsubscribe-auth/AH90SJ6lUo7yaP6QmqsGU1V00pmbYmHBks5qWwTQgaJpZM4JN57J .

paul-shannon commented 8 years ago

Hi Nick,

I’ve been able to use your heat map in my own webapp. I now wish to strip out some of the controls you offer, these in particular (starting with the x button and “Share the visualization..”).

Where can I read in order to learn to do that?

Thanks!

On Jul 18, 2016, at 2:52 AM, Nicolas Fernandez notifications@github.com wrote:

Paul,

Great, I'm glad that worked out. I agree that python 3.5 support is a good idea and I'll let you know when that is available :)

Thanks for the feedback.

Best, Nick

On Jul 18, 2016 12:45 AM, "Paul Shannon" notifications@github.com wrote:

I installed python 2.7. Everything works great. Very nice software!

If you are so inclined, support for python > 3.5 would be useful to us here at the ISB.

  • Paul

On Jul 17, 2016, at 6:57 PM, Paul Shannon < paul.thurmond.shannon@gmail.com> wrote:

Hi Nick,

Thanks for these answers and suggestions.

Wishing to get a quick start, and deferring R for a while, I just spent some time trying to get clustergrammer.py working on rc_two_cats.txt. Discovering that your code is python 2.7, not 3.5, I hacked my way through a partial revision of your code, hoping to squeak out that quick start. I didn’t quite make it.

Maybe a >= 3.5.1 version of your package is in the works?

Now I will turn to your docs on the json format, so how that goes.

I am eager to use your heatmap. Thanks again.

  • Paul

On Jul 16, 2016, at 10:29 AM, Nicolas Fernandez < notifications@github.com> wrote:

Hi Paul,

Thanks for your interest. I'm still updating the documentation for the JSON format. Here is a link to the current documentation https://github.com/MaayanLab/clustergrammer#clustergrammer-json-format

And here is an example json -

https://github.com/MaayanLab/clustergrammer/blob/master/json/mult_view.json

The format does support hierarchical clustering - each clustergram has 10 hierarchical group levels. You can encode this in the group value. Here's an interactive demo that shows how to interact with the dendrogram here http://amp.pharm.mssm.edu/clustergrammer/

You can also use the clustergrammer.py module to produce the json

https://github.com/MaayanLab/clustergrammer#clustergrammer-python-module

I'll let you know when I've updated the documentation. Please let me know if you have any questions.

Best, Nick

On Fri, Jul 15, 2016 at 10:55 PM, Paul Shannon < notifications@github.com> wrote:

Is there documentation for the json input files? I see row_nodes, col_nodes, links, and reverse engineering the formal structure might not be so hard. But a formal statement of the expected file structure would be very helpful.

For what it's worth, I will be generating matrices in R, sending them as JSON over websockets to the browser.

Is there any support - now, or planned - for hierarchical clustering? It -seems- (to my eye, on first look) that the clustering of rows and columns is more flat than tree-like.

Thanks for this very fine javascript widget.

  • Paul

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/MaayanLab/clustergrammer-web/issues/1, or mute the thread < https://github.com/notifications/unsubscribe-auth/AH90SMnAR50y-bP3dFNep5m8Gf1Pb4w3ks5qWEgQgaJpZM4JN57J

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/MaayanLab/clustergrammer-web/issues/1#issuecomment-233227954, or mute the thread https://github.com/notifications/unsubscribe-auth/AH90SJ6lUo7yaP6QmqsGU1V00pmbYmHBks5qWwTQgaJpZM4JN57J .

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

cornhundred commented 8 years ago

Hi Paul,

That's great. I still need to document more of the controls, but you can get rid of the share, help and camera icons using the optional argument to Clustergrammer.js // define arguments object var args = { root: '#container-id-1', 'network_data': network_data, 'about':'Zoom, scroll, and click buttons to interact with the clustergram.', 'sidebar_icons':false };

The last 'sidebar_icons' part is what you want. Also you can also remove any component in a hacky way using d3 like this

d3.selectAll('.expand_button').remove();

I hope that helps. I'll will let you know when I've updated the documentation.

Best, Nick

cornhundred commented 8 years ago

Paul,

Since you are using the JavaScript and Python code on its own, these questions are more appropriate for the clustergrammer repo here:

https://github.com/MaayanLab/clustergrammer

Currently, we're on the clustergrammer-web repo that hosts the code for

http://amp.pharm.mssm.edu/clustergrammer/

Best, Nick