When I click on any of the transition variables, I get pop-up with no options to select:

Actually, every once in a while, the options are there, but it's intermittent.

Let's move the legend all the way to the left and put the Time axis bar adjacent to all the patients.

1. They appear with a color box.
2. I can't click on them to make them the primary variable used to color the boxes. In the screenshot below I had actually promoted the CDKN2A with the purple box in the other view, but it switches to the non-binary one in the global view

For reference, this is what I have:

I think we need a "Start Over" button. Or, better yet, an undo option!

I think we need a new "grouping" icon, instead of

If I click on the vertical "set to screen height" in global timeline, it zooms in too far and the plot extends beyond the window and i need to scroll down to see the bottom of the plot

Rather than the box next to the variable names, can we have an "x"? That will make more clear that clicking will delete the track

Let's add tool-tips to all the main action icons, e.g. sort, group, etc.

Somewhere, perhaps top right, I think we should add a nicely designed info box that summarizes the data, e.g. study name and description, XXX samples, YYY time points, etc.

There is quote character showing at the left edge of the window below the variable list.

If I try to add a gene without any mutations OR if I try to add a gene which is not actually a gene, there is no response provided to the user.

For a real gene without any mutations, I think we should still add the track. We could perhaps provide the user with a warning/choice about it (e.g. "There are no mutations in XXX. Add track anyway? [yes] [no]") or we can just add it and let the user figure it out.

If the gene that is entered isn't a real gene name, then we should provide a warning to the user, e.g. "XXX is not a valid HUGO gene symbol"

If I log transform a track, apply it, and then return to the "modify continuous variable" page, then the plot of the data shows the log-transformed data but the radio button is set to "None" rather than "log"

I'm not sure why the transition variables have boxes while none of the others do. Can we remove them?

It should revert to the original view upon first loading which includes one track

I was able to group on a continuous variable without binning by directly clicking on "apply group to all timepoints"

Depending on screen width (I think?), this sometimes happens:

If I start with unsorted/ungrouped data...

If I begin by right clicking on the grouping button, and select "apply to all timepoints", it applies the grouping to the timepoint I selected and to all other timepoints.

If I begin by right clicking on the sorting button and select "apply to all timepoints", it doesn't first sort the timepoint I selected and then apply that order to other timepoints, it just applies the current sort order to other timepoints. In order to sort all timepoints by a particular variable, I need to first sort the timepoint of interest and then right click to apply to other timepoints.

While I can understand why this may make sense, my preference would be to have the sort button act more like the group button.

I tried adding EGFR mutations-binary in the glioma study and when I click "add", nothing happens. We used to have a pop-up warning the user that there were no alterations and letting the user decide whether or not to add it.

Since clicking "show relative time" does nothing when data is grouped, let's make the button unclickable

After the user has selected a study, the center of the screen is currently blank. I think it would be better if we auto-selected the first feature instead, so that we orient the user to the interface.

In the LGG dataset, if I add a track for mutations in a gene, the value for samples without a mutation should be wild-type (or not mutated), not undefined.

Rather than having a separate button, how about integrating this feature into the axis label. We could rotate the axis label and add a cogwheel which when clicked brings up radio buttons to select days/weeks/years - something like this:

In heatmap view, add a transition variable and group all timepoints by it (Chemotherapy in the screenshot below)
Go to global timeline view and add another transition variable (XRT in the screenshot below)
Go back to heatmap view - the newly added transition variable (XRT) appears blank:

If I promote XRT, then the coloring is restored:

Following the same procedure with a timepoint variable doesn't have this problem.

This should be rounded a single decimal point

These are so big the text overlaps - I think scientific notation would help here

If I have all data grouped and then delete the transition variable, what remains doesn't look right:

Before:

After:

This should say IL2 PEAK but the end of the word is cutoff. The whole name is visible in the dropdown but gets cutoff when selected.

If I click the gear icon to bring up the bin mutation count pop-up, it shouldn't include the blue text box about binning before grouping since the user isn't trying to group anything. Can that blue text box appear conditionally based on which button the user clicked to open the popup?

With my screen size, I always have the buttons in two rows. Can "Show/Hide global timeline" be moved to be in the row above? Or what about splitting up the buttons so the relative time & global timeline buttons appears where the buttons currently are on the left side of the screen, and the undo/redo/reset buttons appears in the upper right of the screen?

In the tooltip for a data track that is binned, can we show the actual data value also, and not just the bin name? Or have I already asked about this and it was a complicated thing to implement?

When the values for a variable are long, the legends run off the side of the page. This is what I see without any scrolling/window adjustments:

I can scroll to the right a bit, and read more of the legends, but some are still cutoff:

I know that making all the legends fit on the screen without scrolling is a bigger task, but is it an easy fix to at least be able to scroll more to the right, such that all the legends can be read? If possible, that would be helpful before testing tomorrow.

For the horizontal zoom, to zoom in I move the slider to the left and to zoom out I move it to the right. But for the vertical zoom, I zoom in by moving the slider to the right and zoom out by moving it to the left.

I think the vertical zoom is set to the more intuitive orientation, so let's flip the horizontal zoom to match the vertical zoom.

Also, consider adding a "-" and "+" to either size of the slider to make this explicit.

It's not currently clear that time is being represented.

Perhaps, we could simply add two labeled axies, one that says "Samples", and points to the right, and one that say "Time" and points downward. Similarly, we could label each time point, e.g. Time Point 1, Time Point 2, etc.

Can we have a default color scheme for any copy number tracks? Deletions should be blue (deep blue for -2, lighter blue for -1), zero can stay grey, and then gains (+1) should be pink and amplifications (+2) should be red. This is a standard color scheme that people will make interpreting the data much easier for a user.

None of the CIC mutations in this dataset have a VAF. We shouldn't show -infinity to infinity as the heatmap legend - probably there just shouldn't be a legend at all in this case.

ATRX is a valid gene and does appear in the plot after I click ok. The warning shouldn't appear if the gene is lowercase.

I think this sidebar would be clearer to read if there were some blank space above the lines for "Sample Variables" and "Transition Variables".
Also can we capitalize "Variables" in "Transition Variables" for consistency?

Let's keep the legend continuous and not have a big gap between transition variables & timepoint variables:

This tooltip value can be truncated to fewer decimal places, much like the legends now are:

Would be nice if a user could show/hide specific time points.

If I right click on the "group" button, I can chose to group all timepoints.

But once grouped, if I right click on the "ungroup" button, I am still given the option to group all timepoints, but it should be to ungroup all timepoints.

Can this arrowhead rotate when a user clicks it? So it points to the right when closed and then points down (as it does now) when open?

They just look like floating text right now. Can they look like buttons?

From the NIBR extended data study:

The two screenshots below show the same axis labeled in months & years. The 32 months & 2 years labels are in the exact same place -- but 32 months is not the same as 2 years. The labels need to move during unit conversions so they remain accurate.

This happens for tooltips in the plot and also in the clinical feature selection