Update in Multimodel plot functionality #11
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Contributor
curadomr
commented
Aug 30, 2022
curadomr
commented
- getPlottingData provides mapping object, only for provided feature_id.
- testID and modelID must be vectors of same lenght for multimodel plots.
- results for multiple tests from a given model are provided as nested lists in plottingData, within the list element 'result', and named after the corresponding testID
- testPlot.R and vignette/OmicNavigatorAPI.Rnw adapted accordingly.
- getPlottingData provides mapping object, only for provided feature_id. - testID and modelID must be vectors of same lenght for multimodel plots. - results for multiple tests from a given model are provided as nested lists in plottingData, within the list element 'result', and named after the corresponding testID - testPlot.R and vignette/OmicNavigatorAPI.Rnw adapted accordingly.
|
Quick update from our discussion: the plan for the mapping object is to be a list of data frames (one per modelID), similar to features and samples. In most cases there will only be a single mapping table to map featureIDs across all modelIDs of the study. Thus a user can choose the modelID "default" when adding it with |
- multiModel does not require to have testID anymore and it may be set to NULL. In this case, plottingData returns assays, sample and features objects only (no results object). - When testID is provided, it must be a vector of same length of modelID. Not needed to be named vector any longer, but the index position of a test in testID must match the index position of its corresponding model in modelID - mapping object is provided in the plottingData object for multiModel calls - checks for mapping in getPlottingData moved to a function outside getPlottingData to facilitate testing, readability, maintenance - note: some checks are crashing in testGet, testGetNumeric and testPlot. All seem to be related to getMapping, plausibly in the getElements call. Other than that, testCheck, testValidate look good.
jdblischak
suggested changes
Sep 9, 2022
|
@curadomr Before you make additional changes, make sure to pull my commits to your computer first: |
jdblischak
reviewed
Sep 12, 2022
…versions.
- stopifnot("text" = check), from R 4.0, is replaced by regular if () {stop()} calls
- list2env is replaced by explicit variable attribution
- news.md and DESCRIPTION updated
|
I figured out how to fix the errors related to missing values in character columns. I'm going to merge this first and then push my fix. |
jdblischak
approved these changes
Sep 13, 2022
|
Thanks @curadomr! |
|
Support for missing values in character columns added in bc3a831 |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.