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jamiewaese / ePlant

ePlant is a data visualization tool for integrating and exploring multiple levels of biological data.
MIT License
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In cyctoscape view, hovering or clicking on protein should bring up the annotation popup. #50

Closed jamiewaese closed 11 years ago

jamiewaese commented 11 years ago

Have we discussed this already? Sounds familiar. Anyhow, it just occurred to me again.

If you feel the popup would be too intrusive on the display, perhaps we should add an information panel on the right side along with tool specific options. Like this...

cystoscapeinfobox

yuzhenmi commented 11 years ago

Yeah I think you mentioned this before. It's definitely on my to-do list. In fact I'll probably start on this tomorrow.

I feel adding an information panel would take up a lot of space. I personally like the view-specific options in the bottom better.

I'll duplicate the AnnotationPopup class I have for ChromosomeView for this. At one time I thought it would be a nice idea to let different views share the AnnotationPopup class but I think it's better to have a separate one for each view so that we can customize them later. There are so many types of data about the gene that we can show on the popup after all, and I think some would be more appropriate for some views.

By the way, it would be nice to give me as much information as possible regarding the visual design and features for this view. It's always better to plan out the class structure than to go back and edit it.

yuzhenmi commented 11 years ago

From the top of my head, we would probably want to include most features from the AIV: filtering options, legend, custom data? data download? table of PPI (I don't think the table is necessary if we include all the information in the view)?

yuzhenmi commented 11 years ago

Hovering/clicking on a node would bring up something like the annotation popup, but hovering/clicking on an edge would bring up data for the particular interaction (basically the data in the table).

jamiewaese commented 11 years ago

Excellent.

On Oct 30, 2013, at 1:27 AM, Hans Yu notifications@github.com wrote:

Hovering/clicking on a node would bring up something like the annotation popup, but hovering/clicking on an edge would bring up data for the particular interaction (basically the data in the table).

— Reply to this email directly or view it on GitHub.

jamiewaese commented 11 years ago

Nick - Is there an implementation of Cytoscape that is particularly good that I can look at for ideas on how we should layout our viewer? Can you send a link?

Also, which features are on your "must have" list?

On 2013-10-30, at 1:21 AM, Hans Yu wrote:

Yeah I think you mentioned this before. It's definitely on my to-do list. In fact I'll probably start on this tomorrow.

I feel adding an information panel would take up a lot of space. I personally like the view-specific options in the bottom better.

I'll duplicate the AnnotationPopup class I have for ChromosomeView for this. At one time I thought it would be a nice idea to let different views share the AnnotationPopup class but I think it's better to have a separate one for each view so that we can customize them later. There are so many types of data about the gene that we can show on the popup after all, and I think some would be more appropriate for some views.

By the way, it would be nice to give me as much information as possible regarding the visual design and features for this view. It's always better to plan out the class structure than to go back and edit it.

— Reply to this email directly or view it on GitHub.

yuzhenmi commented 11 years ago

I've implemented annotation popup, triggered by hover or click on a node.

For views other than Species and Chromosome, the data of the selected gene should not be dropped. For now, I have the Drop Data button's label changed to "Disabled" for the selected gene. Do you have any better ideas to deal with this? I can change the style of the button (no hover) but I can't seem to disable or change the hover behaviour because it does not seem to be associated with the HTML element.

Also, I will make the view icons in the popup clickable, in case you are wondering (for both ChromosomeView and InteractionView).

yuzhenmi commented 11 years ago

I think hovering and clicking on a node should give it an outline (darker in color?). Also, the nodes that are loaded should have a different color.

yuzhenmi commented 11 years ago

Having the option to choose coloring scheme would be nice too. E.g. by default (as it is currently), by compartment, by type of evidence (edges), by expression, etc.

yuzhenmi commented 11 years ago

For this view, pinning the annotation popup when the mouse is between the popup and a node seems annoying to me. How about we disable this feature? The user can click on the node if they want to access the annotation popup. That way people won't have to maneuver their mouse all over the place just to get rid of the popup so that they can check out other nodes.

yuzhenmi commented 11 years ago

Jamie, can we have a Skype discussion about what to do for the Cytoscape/interaction view sometime soon? Thanks!

jamiewaese commented 11 years ago

Yes. How is tomorrow morning for you? I'm free all day so name the time.

On 2013-10-31, at 7:17 PM, Hans Yu notifications@github.com wrote:

I've implemented annotation popup, triggered by hover or click on a node.

For views other than Species and Chromosome, the data of the selected gene should not be dropped. For now, I have the Drop Data button's label changed to "Disabled" for the selected gene. Do you have any better ideas to deal with this? I can change the style of the button (no hover) but I can't seem to disable or change the hover behaviour because it does not seem to be associated with the HTML element.

Also, I will make the view icons in the popup clickable, in case you are wondering (for both ChromosomeView and InteractionView).

— Reply to this email directly or view it on GitHub.

yuzhenmi commented 11 years ago

How about 11 am in Toronto? It would be 9 am for me.

jamiewaese commented 11 years ago

Perfect.

On 2013-11-04, at 1:49 PM, Hans Yu notifications@github.com wrote:

How about 11 am in Toronto? It would be 9 am for me.

— Reply to this email directly or view it on GitHub.