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Sage-Bionetworks / projectLive_NF

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User feedback : Internal stakeholders #119

Closed jaybee84 closed 3 years ago

jaybee84 commented 3 years ago

Is your feature request related to a problem? Please describe. We want to get your preliminary feedback on the Milestone Tracker submodule. Please check out the plots in the Participating Studies module in the staging site

Describe the solution you'd like

Describe alternatives you've considered Note: a new issue (#118) is open to make the colors of the bars for a specific fileformat consistent within the Milestone tracker subplots

kthrog commented 3 years ago 
Is anything wrong with the plots?

It's a bit unfortunate when I get one that's unspecified. I'm not sure a funder would know what that means (I assume it means it's not yet annotated, and thus doesn't have a data type yet.) Or I suppose, my question is, what is the label pulling from for each individual plot? In a couple I tried, I got html as one, which was a bit odd (this was on the study, "Microenvironmental Targets of Cutaneous Neurofibromas", milestone 2). I think data type or assay might make more sense than file format. 

Does it convey what you want to track?

Overall, yes. I like the internal and researcher-reported sections; I think this helps convey multiple kinds of information easily. 

How can we improve the viz?

I will admit, it took me a minute, in the internal milestone module, to figure out that I needed to click one of the rows to the right showing milestone / dates to see a visualization. I worry that if it took me a moment to process how to do that, it might take our funders a bit more time. Maybe some instructions, just below the 'internal milestone tracker' would be nice (e.g., click a milestone number from the table on the right to see a visualization of expected and actual data)? Also, the 'specify number of days' is a bit confusing to me here. I assume most people would want to see all deliverables in accordance with milestones so far. If possible, I might display a plot set to default amount (365 days perhaps?) first, and then allow the user to reconfigure if desired.

allaway commented 3 years ago 
Is anything wrong with the plots?

I'm a little confused by the day-selector. Is this just days in history starting from today? It seems to change the visualization for every milestone plot, which is a little confusing. I agree with kaitlin, I think milestones should be by data type or assay (at least, I thought that's how we were tracking them?) 

Does it convey what you want to track?

I like the researcher-reported milestone best. I think this visualization is what a funder would be expecting. I'd actually put this first. 

How can we improve the viz?

I, like kaitlin, didn't realize at first that I could click a row to get plots (actually, I didn't figure it out until I read her comment). I'd also remove the row index from the table in the "internal" section - it's a little confusing next to the milestone numbers. I agree with Jineta's comment somewhere else, not sure where I saw it, that the palette should be match to the same values, at least within each box. Instead of a dropdown in the Researcher Reported milestone section, to reduce the number of clicks since there are only a few simple options, I'd suggest radio checkbox or radio button....I'm partial to shinyWidgets: http://shinyapps.dreamrs.fr/shinyWidgets/

Nice work all, I think that this will be very useful!

jaybee84 commented 3 years ago

thanks all !

re: choice of plotting fileFormats instead of resourceType or dataType or assay The choice to not plot resourceType or dataType was a conscious one. We want to make sure that investigators are uploading correct fileformats for each datatype. If an investigator uploads an excel file and annotates it with geneExpression (as resourceType) for a milestone, plotting the resourceType will show the milestone is fulfilled but actually uploading the correct fileFormat will still be unmet.

  • maybe a happy medium could be adding the resourceType as a tooltip on hover.

re: unspecified This shows unannotated files or entries in the data sharing plans that did not specify a file type

re: adding instructions to click on a row to view the milestone @andrewelamb : I tried to add header text to the config file for these two plots, but it did not render. Could you add that user functionality to this module?

re: day selector @allaway : this day selector acts as a sliding window with the center around the milestone upload date (i.e. if no. of days = 60, the milestone reporter checks files uploaded in the time window of milestone date +/- 60 days for all milestones.

jaybee84 commented 3 years ago

@andrewelamb : TODOs from above feedback:

  1. In the Internal Milestone Tracker, a slider bar may be a better choice for the day selector.
  2. The day selector should be placed after the milestone date table
  3. To clarify the dates and time windows in the milestone date table, lets rename the columns to say: Milestone Number, Designated upload date, Search window start date, Search window end date
  4. Place Researcher reported milestone tracker before Internal Milestone tracker

  5. 118

  6. Ability to add header text to each of these new plots.
  7. Add ability to view resourceType as additional tooltip to the plots
allaway commented 3 years ago

"maybe a happy medium could be adding the resourceType as a tooltip on hover."

How about the other way around, or adding an additional facet by fileFormat? I think my concern w/fileFormat: this is something we can interpret (e.g. we expect a fastq or a bam for geneExpression), but I don't know that a funder representative will necessarily be able to make that leap. I think a dataType (which is what they are trying to compare from the data sharing plan to reality) would be easiest for them to use.

One other thing I missed on the first pass:

The "Researcher reported milestone tracker" plots could be improved by being either be one single grouped barplot (grouped by dataType, so that it's easier to compare expected vs actual), or if they stay two plots, the y-axes should be the same scale (right now they are free, so more difficult to directly compare Expected vs Actual.

Cheers, Robert

On Thu, Apr 15, 2021 at 2:25 PM Jineta Banerjee @.***> wrote:

thanks all !

re: choice of plotting fileFormats instead of resourceType or dataType or assay The choice to not plot resourceType or dataType was a conscious one. We want to make sure that investigators are uploading correct fileformats for each datatype. If an investigator uploads an excel file and annotates it with geneExpression (as resourceType) for a milestone, plotting the resourceType will show the milestone is fulfilled but actually uploading the correct fileFormat will still be unmet.

  • maybe a happy medium could be adding the resourceType as a tooltip on hover.

re: unspecified This shows unannotated files or entries in the data sharing plans that did not specify a file type

re: adding instructions to click on a row to view the milestone @andrewelamb https://github.com/andrewelamb : I tried to add header text to the config file for these two plots, but it did not render. Could you add that user functionality to this module?

re: day selector @allaway https://github.com/allaway : this day selector acts as a sliding window with the center around the milestone upload date (i.e. if no. of days = 60, the milestone reporter checks files uploaded in the time window of milestone date +/- 60 days for all milestones.

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jaybee84 commented 3 years ago

I like the idea of additional faceting by fileFormat and dataType/resourceType, so have a dropdown list where user can choose what they want to facet by. We can make the dataType facet default and then user can choose fileFormat for additional info.

The "Researcher reported milestone tracker" plots could be improved by being either be one single grouped barplot (grouped by dataType, so that it's easier to compare expected vs actual)

We had the two plots to distinguish it from the Internal tracker which is a single plot faceted by fileFormat.

y-axes should be the same scale

Agree

jaybee84 commented 3 years ago

Hi All,

Please take a look for round 2 of review: https://shiny.synapse.org/users/jbanerjee/testprojectlive/

Describe the solution you'd like

allaway commented 3 years ago

Looks great! I think this is ready to demo with external stakeholders. I would suggest starting with Sang to get his feedback.

allaway commented 3 years ago

The only improvement that I see that is remaining is to annotate the data so that the plots show up. Can I help with that? I'm working on doing this for the Genetic Studies of NF project right now anyway...

jaybee84 commented 3 years ago

Happy to set up some time with Sang to demo this.

Re: annotation: definitely would need your help on that. I think we just need to go down the list of all studies to add the reportMilestones and dataTypes. We can start with these studies listed in the incomingData Table