sanoke/hetviz

Treatment Effect Heterogeneity visualization using R

hetviz's Issues

Deactivate UI elements that shouldn't be used at a certain time

Use Javascript (or, worst-case scenario, a color change) to deactivate user elements that shouldn't be accessed at certain points of UI interaction.

• When the user presses the Generate visualizations button, the UI elements of the sidebar should be deactivated, including the Generate button itself.
• The Reset button should be deactivated until the user presses the "Generate visualizations" button.
• When the user presses the Reset button, the UI elements of the sidebar should be reactivated (need to fix other behaviors of the Reset button -- see #8).
• In the Forest Plot tab, if the dataset is too "large", deactivate the option to plot data at the individual-level.
• In the Forest Plot tab, use JavaScript to indicate to the user untenable plot option combinations (moved from sanoke/hetviz-dev#39).
• In the Subgroup Profiles tab, use JavaScript to indicate to the user untenable plot option combinations.

In subgroup-level plotting of "Forest Plot", correct error plotting

The whiskers of the "boxplots" are calculated as 1.5*IQR, regardless of whether there's actually a datum out there. This needs to be corrected.

On their side of the middle 50%, the whisker should stop at the value that is \leq 1.5*IQR.

Add adjustable highlight band to subgroup profiles + covariate profiles

Add an adjustable horizontal highlighting bar to the Subgroup Profile tab and the Covariate Profile tab. This will help the user more clearly see deviations.

In the Subgroup and Covariate profiles tab, figure out a better presentation

At the moment, everything is plotted all at once. Is there a better way?

• Animation, cycling through the covariates?
• Construct a "select all" / "select none" functionality?

Clean up internal documentation of code for v1.0

Want to add in some better internal documentation.

Add better documentation within the UI

Within each pane, write in some comments + an example screenshot of what the user should expect to see. This includes information on the calculations used to generate the plot. This will be in the User Manual, and a link to the appropriate page will be provided in the UI.

• Add description of the Forest Plot tab
• Add description of the Subgroup Profile tab
• Add description of the Viz by Subgroup tab
• Add description of the Covariate Profile tab
• Add description of the Viz by Covariate tab
• Add overview of how to use the app

`ggplotly()` not allowing the user to download plots

When the user presses the "download plot" button (looks like a camera), an error message appears.

Make progress bar updates more accurate

At the moment, the progress bar update amounts are somewhat arbitrary. Would like to write a function to determine how much to increment (which is dependent on what type of plot is being generated) and use that function to do the increments.

Data preview with complex simulated data

Should it be empty?

Fix weird warning message in "Viz by Covar" tab

The correct figure is generated, but a weird error is printed to the console. It also looks like the app is doing calculations twice...?

Warning: Error in eval: incorrect length (0), expecting: 9215
Stack trace (innermost first):
    96: <Anonymous>
    95: stop
    94: filter_impl
    93: filter_.tbl_df
    92: filter_
    91: as.data.frame
    90: filter_.data.frame
    89: filter_
    88: dplyr::filter
    87: eval
    86: eval
    85: %>%
    84: vizByCovar [/Users/Baloo/GitHub/hetviz-dev/R/vizByCovar-plotFcn.R#194]
    83: eval [/Users/Baloo/GitHub/hetviz-dev/inst/shiny/server.R#519]
    82: eval
    81: withProgress
    80: "plotly"::"ggplotly" [/Users/Baloo/GitHub/hetviz-dev/inst/shiny/server.R#517]
    79: func
    78: origRenderFunc
    77: output$vizByCovar
     2: shiny::runApp
     1: hetviz [/Users/Baloo/GitHub/hetviz-dev/R/runShinyApp.R#18]

How to calculate the standard error of a polytomous covar?

I've been conflating the identification of dichotomous and polytomous covariates -- because they've been the same in the test data I've been using.

But at some point, I will need to separate this out and handle them differently.

• In Subgroup Profiles, need to add calculations for the mean and SE of a polytomous variable.

Final steps...

• Add the corrected functionality to the User Manual (at the moment, UM indicates there's only support for binary covariates).

Construct data for "complex data" option

• Construct synthetic data from the CER analysis
• Find two real clinical trial data sets.
• Construct synthetic datasets from the two real datasets.
• Provide script for user to generate these two synthetic datasets (in separate branch).
• Document this script in the User Manual.

Subgroup info displayed twice in line plot

New incompatibility between ggplot2 + plotly + shiny widget IDs

When generating the forest plot, get a new error:

> hetviz()

Listening on http://127.0.0.1:6353
Warning in origRenderFunc() :
  Ignoring explicitly provided widget ID "95a4fa9b92a"; Shiny doesn't use them

Shiny was updated a few days ago and there's at least one person reporting the same error.

Improve coverage

https://codecov.io/gh/sanoke/hetviz

Change distance calculations from marginal SEs to marginal SDs

Convert included simple simulated data to a tibble

• Use readr::as_tibble()
• Document the data as tibble
• Simplify all the ifelse() syntax that was checking whether the passed data is a data.frame or a tibble

Implement the ability to read data from relational databases

Would like the app to be able to connect to a remote database, and pull data for visualization.

plotly::renderPlotly() takes several seconds to load w/ no notice to user

The initial plot takes a while to load, as does any modifications to the plot.

• e.g., de/selecting a subgroup in the "Subgroup Profiles" panel

withProgress() doesn't help, because I would need to add incProgress() calls within the definition of plotly::renderPlotly().

So, need to research how to display some sort of busy signal to the user while the plot completes its rendering.

Fix behavior of reset button

• Clear out text input boxes in the Data Preview tab
• Clear out printing of variable names in the 'Data Preview' tab
• Clear out name of file in File Upload section, in sidebar
• Reset 'Data source' UI element to simple simulated data
• Clear out any dataset that is 'loaded' into the app.

Replace exportPattern() in NAMESPACE with roxygen2 @export

Creation of user-generated summary document

Would like the user to be able to create a summary document of plots and annotations from the application. Will need to put some thought into what this document will look like. But it will contain (list updated regularly):

• Date / time of document creation
• Name + version # of hetviz
• Figures from the exploratory analysis, as selected by the user (these figures will be separated into sections, corresponding to the tabs in the UI).

plotly::ggplotly() analog to ggvis::bind_shiny()

plotly::ggplotly() doesn't have an analog to ggvis::bind_shiny()... in other words, it's not possible to dynamically create plotly plots, although it is in ggvis (e.g., each iteration of a for() loop generating a plot whose name depends on the iteration number of the loop).

So for now, I will use ggvis() but make a note for the future to program this functionality myself (this is a nontrivial task) and/or suggest to the plotly developers to create such a function.

[Moved from sanoke/hetviz-dev#44]

Write function that (re)assigns group numbering by increasing subgroup TE

Put the function definition in R/summaryFcns.R and add it to the dataCompat() definition, where data is prepared for plotting.

Update instructions on how to install app

Write helper function to calculate marginal means and SEs

This calculation is done for most of the features, so a function should be written to do this, and the results cached.

Can do this calculation inside the observeEvent() for the start button.

[Moved from sanoke/hetviz-dev#40]

To profile plots, add button to omit small subgroups

... let the user define what "small" is?

Such a button is important because the small subgroups are often the ones with the extreme values, and can be distracting within the plot.

Construct forest plot behavior for when the user has not specified an estimated ITE

There are two options here.

1. Write behavior to accommodate when the user does not have an estimated ITE -- this would be to calculate the subgroup treatment effect as the difference in outcome means across treatment arms.
2. Tell the user that they have to provide an estimated ITE to have access to the Forest Plot tab; disable the tab otherwise.

Will ask @czigler and @cchoirat about this.

Cache plots so that they are not regenerated when the user requests a second time

Plots with a lot of subgroups and/or observations take a long time to generate, and caching would help speed things up.

PostgreSQL password info should be masked

Fix outcome variable and treatment variable axis labels in plots

When a dataset is loaded, the names of certain variables (outcome, treatment, subgroup indicator, estimated ITR (if provided)) are changed to be compatible with some hard-coding.

These 'new' compatible names are contained in plots containing these data. Instead, these plots should display the name contained in the user's data.

Better consideration if invalid/empty subgroup

[An issue in the 'Viz by Subgroup' tab]

This issue is indicative of a larger problem, ensuring that the variable containing subgroup membership is coded properly.

Proper coding means that this variable takes consecutive integer values, starting at 1. Groups are numbered in order of increasing subgroup-specific average treatment effect (ATE).

At the moment, proper coding is an assumption, and I need to write a function to enforce it. If there's an empty subgroup / invalid subgroup number, no plots will display. (There's a notice to this effect in the panel.)

• Write function to check that grouping variable is coded properly. Do group reassignment if needed.

In the interim, I'll provide a script for the user to do this check themselves. Eventually I will do this check within my application, and do some reassignment as needed.

In 'Data Preview' for user-provided data, use drop-downs instead of text boxes

The initial thought was that typing the name of the variable would be faster than scrolling through a long list. Will need to get feedback on this...

Construct a demo version of the app for shinyapps.io

On GitHub, this demo version will live in its own branch. It will demonstrate functionalities on simulated data (user will have to download app to run on actual data).

[Moved from sanoke/hetviz-dev#46]

Clean up "subgroup profile" horizontal line plotting

• The horizontal lines have points on the left and right of the plot, that need to be hidden.
• Add details about what the horizontal lines are.

[Moved from sanoke/hetviz-dev#38]

Travis builds are ignoring the instructions of `.Rbuildignore`

TravisCI is including files in its package builds that it's not supposed to be (as per .Rbuildignore). Not sure if this is an issue of settings on my part or a bug within Travis.

Edit the tool tips in all plots to be more informative

At the moment the tooltip contains ggplotly() default text. This text needs to be revised to contain more helpful information.

[Moved from sanoke/hetviz-dev#7]

Write function to ensure / create proper group coding

[Related to #24]

Proper subgroup coding means that this variable takes consecutive integer values, starting at 1. Groups are numbered in order of increasing subgroup-specific average treatment effect (ATE).

At the moment, proper coding is an assumption, and I need to write a function to create/enforce it. If there's an empty subgroup / invalid subgroup number, no plots will display. (There's a notice to this effect in the panel.)

Write function to check that grouping variable is coded properly. Do group reassignment if needed.
In the interim, I'll provide a script for the user to do this check themselves. Eventually I will do this check within my application, and do some reassignment as needed.

App crashes when user-provided data is selected but no data is provided

Trying to generate viz with user-provided data selected and no data actually uploaded crashes the app:

Warning: Error in if: argument is of length zero
Stack trace (innermost first):
    66: observeEventHandler [/Library/Frameworks/R.framework/Versions/3.4/Resources/library/hetviz/shiny/server.R#120]
     2: shiny::runApp
     1: hetviz [/Users/cchoirat/Documents/LocalGit/hetviz/R/runShinyApp.R#20]

Change median plot character in subgroup-level Forest Plot

At the moment, the character is a small hollow circle. Would like this to be a filled circle.

Add CodeCov and TravisCI buttons