Assorted cosmetic changes

[dondi]

Some items that were not already transcribed from Thursday’s whiteboard notes:

• Put self-referring arrowheads on the bottom side of the rectangle, and not the right
• Set rectangle and edge thickness to 2px
• Display border around embedded graph/artboard

[britainjs]

I implemented the 1st two of the list.

[dondi]

• Put self-referring arrowheads on the bottom side of the rectangle, and not the right
• Set rectangle and edge thickness to 2px
• Display border around embedded graph/artboard

For the first bullet, we will go with custom markers for each thickness because the automatic way blows them up too much.

[dondi]

So as not to have too many custom markers, explore whether a transform can be applied.

[britainjs]

Adjusting the radius of the self-referencing edges and adding an offset to compensate for the larger sizes inadvertently solved the orientation issue, so the self-referencing arrowheads look pretty good now.

[kdahlquist]

The demo is not working for me so I can't see the changes. I used this file: dahlquist_wt-data_21-gene- sample-output_20140122_est_out_1.xlsx

At 04:07 AM 4/20/2014, you wrote:

Adjusting the radius of the self-referencing edges and adding an offset to compensate for the larger sizes inadvertently solved the orientation issue, so the self-referencing arrowheads look pretty good now.

— Reply to this email directly or https://github.com/dondi/GRNsight/issues/38#issuecomment-40892650view it on GitHub.

[britainjs]

I was waiting until I had the flat arrowheads done to update the demo page so we didn't have a half-finished patch on public display, but those are done now and the server is updated. I checked with the output file and it was working like intended. The sizes for all the arrowheads are manual now, so getting the right size and offset is just going to be a matter of adjusting numbers. I experimented quite a bit before I found the current settings, which I tried to make a balance between having a noticeable difference between node sizes and still looking acceptable. Sizes larger than where they are tended to make the markers and edges overlap too much and smaller arrowheads would get eclipsed by the edges they were attached to. Let me know how this looks and I can do more adjustments.

[dondi]

State of prior refinements, all done:

• Put self-referring arrowheads on the bottom side of the rectangle, and not the right
• Set rectangle and edge thickness to 2px
• Display border around embedded graph/artboard

New cosmetic refinements:

• Decrease self-referential radius by around 10-20%
• Set a distinct stroke and fill for markers and edges so that multiple edges that are thick and close
• Highlight connected edges (in or out) on mouseover
• Increase font size of node labels

[britainjs]

• Reduced self-referential radius by 15%
• Stroke and fill did not work due to the behavior of paths. Instead I used filters for a similar effect. This does cause a bit of performance slowdown.
• Highlight functionality added for edges originating from the target. To preserve performance the highlighting is done when a node is dragged rather than on mouseover.
• Font size increased to 18px

[dondi]

• Reduced self-referential radius by 15% —Go another 15%
• Stroke and fill did not work due to the behavior of paths. Instead I used filters for a similar effect. This does cause a bit of performance slowdown. —Look into optimization later
• Highlight functionality added for edges originating from the target. To preserve performance the highlighting is done when a node is dragged rather than on mouseover. —Use orange as a color, and highlight both directions from/to a node
• Font size increased to 18px —Restore vertical centering

[britainjs]

• Reduced self-referential radius by another 15%.
• Highlight color changed to orange and highlights added to incoming edges as well.
• Vertical centering restored.

[kdahlquist]

I can't connect to the server to see these:

Firefox can't establish a connection to the server at grnsight.cs.lmu.edu:3001.

At 03:13 AM 5/5/2014, you wrote:

• Reduced self-referential radius by another 15%.
• Highlight color changed to orange and highlights added to incoming edges as well.
• Vertical centering restored.

— Reply to this email directly or https://github.com/dondi/GRNsight/issues/38#issuecomment-42174619view it on GitHub.

[dondi]

I visited grnsight.cs.lmu.edu and Britain took ownership of the server processes—Britain, you only have one node process running. You need two, one for the web service and the other for the web client. I think that is the issue.

[britainjs]

Weird, I could have sworn I tested both of them before logging out of the server. I'll get it up right now.

-----Original Message----- From: dondi notifications@github.com To: dondi/GRNsight GRNsight@noreply.github.com Cc: britainjs bsouthwi@lion.lmu.edu Sent: Mon, May 5, 2014 12:14 pm Subject: Re: [GRNsight] Assorted cosmetic changes (#38)

I visited grnsight.cs.lmu.edu and Britain took ownership of the server processes—Britain, you only have one node process running. You need two, one for the web service and the other for the web client. I think that is the issue. — Reply to this email directly or view it on GitHub.

[britainjs]

Its up. I think I left the ssh connection open on my computer without detaching the screen, so it complained when my computer went to sleep.

[kdahlquist]

Closing issue and opening separate issues for things unresolved.