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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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A few more items for your to do list... #73

Closed jamiewaese closed 10 years ago

jamiewaese commented 10 years ago

SPECIES SELECTOR Adjust Arabidopsis plant position to the right so we zoom right into it.

CHROMOSOME VIEW CANVAS LABEL If no genes are currently loaded (like when you've just come to the site for the first time) we should add a message in the top center of the canvas that says "Load some genes" with the same green font as the "Select a plant" message on the previous page. If at least one gene is loaded, that message should go away.

ICON DOCK Nick and I were talking about the logic of our view hierarchy. The Chromosome Selector icon isn't in the right place. We should move it lower in the dock to reflect the relative scale of each view. I think the most logical spot is between the Cell eFP viewer and the Cytoscape interactions view. We zoom from the cell into the nucleus to see all the chromosomes. We select a gene of interest, then zoom in further to see its friends and neighbours. From there we continue down to the a 3D view and ultimately the sequence data. The zoom directions shouldn't change.

Here are some icons to go at the very bottom of the dock for the External Tools view. This should bring up a menu page like the Species Selector (use a temp image for now... send me the image size required and I'll create nice placards for each tool). A bunch of Arabidopsis link outs are given in an XML document I'll send by email. externaltools-available externaltools-unavailable externaltools-active We should probably add this to the annotation popup mini toolbars too.

HISTORY PANEL I'm wondering if the labels in the history panel are sufficiently descriptive. Shouldn't they include the GOF that was shown at each view? Suppose you want to go a couple steps back to a view when you were looking at a different gene. Can you add the GOF to the history panel steps?

I think the species viewer should use the same convention of species name first. It anticipates the day when people can compare multiple species in one session.

Let's change the label of Species viewer to Plant eFP

Let's change the label of "chromosome viewer" to "Chromosome view"

If we're greying out the screen behind the history panel, we may as well lock it into place. No point in making it free floating if you can't work while it's up.

eFP STYLING When highlighting a shape, let's use black instead of green for the stroke color. The green clashes with the fill color. It looks good with black in the Processing version.

Can you add a pixel or two of padding to the bottom, left and right sides of the data popups? There's more room at the top (even if it's numerically the same) and it doesn't look balanced.

Can you add a small drop shadow behind the data popups?

When you click on a tissue, there ought to be an alert message asking if the user wants to open the Affymetrix page with links to the raw data.

I'll send a new SVG file asap.

DROPSHADOWS ON ANNOTATION POPUPS Can you add a small drop shadow behind the annotation popups?

yuzhenmi commented 10 years ago

RE History Panel:

The gene of focus is already shown for views that are specific to a gene. ChromosomeView is associated with the species and SpeciesView is associated with nothing.

I am, however, not very satisfied with the internal architecture of the history panel feature, I kind of just whipped it up in a few hours. Currently, it only keeps track of the sequence of views that were active, with zero additional information. I plan to rework it in the future.