NEWS.md

• export of model metadata to JSON now follows the convention NA -> null

• Added citation info to package and readme now references journal article

• Update getPlottingData, plotStudy, and addPlots manuals

1.13.22

• The release tarball includes version 1.9.4 of the web app

1.13.21

• The release tarball includes version 1.9.4 of the web app

1.13.20

• The release tarball includes version 1.9.3 of the web app

• Fix bug in importStudy() that resulted in mapping table not being imported.

1.13.19

• The release tarball includes version 1.9.2 of the web app

1.13.18

• The release tarball includes version 1.9.1 of the web app

1.13.17

• The release tarball includes version 1.9.0 of the web app

• Update getBarcodeData() to pass lowest statistic value. Change enables barcode plot to accommodate negative numbers.

1.13.16

• The release tarball includes version 1.8.9 of the web app

1.13.15

• The release tarball includes version 1.8.8 of the web app

1.13.14

• The release tarball includes version 1.8.7 of the web app

1.13.13

• Add the appropriate PKGNAME-package \alias to the package overview help file as per "Documenting packages" in R-exts

• Update invalid URLs in documentation and tests

1.13.12

• The release tarball includes version 1.8.4 of the web app

1.13.11

• The release tarball includes version 1.8.3 of the web app

1.13.10

• Update check.R, function checkEnrichments to test if enrichments object have columns 'nominal' and 'adjusted' with numeric values (required).

1.13.9

• The release tarball includes version 1.8.1 of the web app

1.13.8

• The release tarball includes version 1.8.0 of the web app

1.13.7

• The release tarball includes version 1.7.9 of the web app

1.13.6

• The release tarball includes version 1.7.8 of the web app

1.13.5

• The release tarball includes version 1.7.7 of the web app

1.13.4

• The release tarball includes version 1.7.6 of the web app

1.13.2

• The release tarball includes version 1.7.5 of the web app

• Added optional arguments annotationID and termID to getResultsTable() to filter the results table to only include features in a given annotation term

1.12.4

• The release tarball includes version 1.7.4 of the web app

1.12.3

• The release tarball includes version 1.7.3 of the web app

1.12.2

• The release tarball includes version 1.7.2 of the web app

• Update mapping data to behave in the same way as the features, samples, etc. Each element of the list must be named after a modelID or "default" to be shared across multiple modelIDs (implemented by Marco Curado in PR #12)

1.12.1

• Bug fix: Support missing values in character columns. Previously they were read as empty strings (""). This update applies to all new as well as existing study packages (ie it is backwards compatible) (reported by Marco Curado)

1.12.0

• Update addMapping() to add the mapping object as a list of data frames, where each data frame consists of a distinct mapping. Mapping object is required for plots combining features from multiple models (multiModel plots) (implemented by Marco Curado in PR #11)

• For multiModel plots, getPlottingData() returns a nested list where elements are named after modelIDs, and each list element contains at least assays, samples and features objects for the given modelID. If testID is passed to the function, it also returns the results for the provided testIDs. In this case, testID is required to be provided as a vector of the same length of modelID, where the index positions indicate which testID relates to which modelID (implemented by Marco Curado in PR #11)

1.11.8

• The release tarball includes version 1.7.1 of the web app

1.11.7

• The release tarball includes version 1.6.9 of the web app

1.11.6

• The release tarball includes version 1.6.8 of the web app

1.11.5

• The release tarball includes version 1.6.7 of the web app

• Bug fix: Do not allow empty sub-lists when adding elements that require a nested list (e.g. addEnrichments()). This can cause problems for exportStudy()/installStudy(), and make it appear that data is available when there is none (reported by Liang Jin and Brett Engelmann)

1.11.3

• The release tarball includes version 1.6.6 of the web app

1.11.2

• The release tarball includes version 1.6.5 of the web app

1.11.1

• The release tarball includes version 1.6.4 of the web app

• New function combineStudies() to combine two or more studies

1.10.5

• The release tarball includes version 1.6.3 of the web app

• Update importStudy() to support study packages that don't have a Maintainer listed. This was only possible prior to version 1.2.0.5. After that, any study that hasn't explicitly provided a maintainer (and maintainer email) is assigned the maintainer Unknown <unknown@unknown> during export. It is highly recommended to set the maintainer name and email for any study package that will be shared. Furthermore, exportStudy() will send a message when no maintainer email has been provided for a study package

• Fix infamous drop = FALSE bug in getUpsetCols(). Previously, if the results tables for a given modelID only had two total columns (the featureID column and one data column), getUpsetCols() returned no common columns, and thus disabled the set interaction features in the app (reported by Brett Engelmann)

1.10.4

• The release tarball includes version 1.6.2 of the web app

1.10.3

• The release tarball includes version 1.6.1 of the web app

1.10.2

• The release tarball includes version 1.6.0 of the web app

• Detect custom plotting functions with plotType == "plotly" that don't properly return an object with class "plotly"

1.10.1

• The release tarball includes version 1.5.0 of the web app

1.10.0

• Support for custom plotly plots. Include the plotType "plotly" to add custom functions that return interactive plotly graphs (implemented by Joe LoGrasso in PR #9) Front-end support will be added in a future release of the web app

• Bug fix: Detach packages in reverse order to avoid dependency conflicts. Explanation: when plotting with plotStudy(), any required packages are attached temporarily and then detached. When one package "Depends" on another package (e.g. plotly Depends on ggplot2), the first package must be detached before its dependency can be detached. Now this dependency order is taken into account when detaching the packages (reported by Joe LoGrasso)

1.9.1

• The release tarball includes version 1.4.1 of the web app

• Breaking change: The function plotStudy() now invisibly returns the result from the custom plotting function. Previously it invisibly returned the study object. It's unlikely you relied on this behavior. For a ggplot2 plot, the return value will be the plotting object with class "ggplot".

1.8.0

• Support for new plotType multiModel. This will enable visualizations between models of a given study. See the User's Guide for instructions. Note that currently this is only supported when calling plotStudy() in the R console. Support for multiModel plots in the app will be implemented in a future release. For now, the app will send a harmless error if it encounters a multiModel plot (implemented by Marco Curado in PR #8)

1.7.1

• The release tarball includes version 1.4.0 of the web app

1.7.0

• New study element mapping for mapping featureIDs across models of a study (see ?addMapping and getMapping). This will make it possible to create plots that combine data across models, which will be enabled in future versions (implemented by Marco Curado in PR #7)

• Bug fix: The validation of the enrichments table linkouts was too strict. It required that the annotationID be present in the annotations created by addAnnotations(). This extra information about the annotationID is only required for the network view. The validation now only throws an error if the annotationID was not included for at least one modelID in the enrichments data added with addEnrichments() (reported by Anastasia Galperina)

• Bug fix: Now that custom plots can include data from the results table, it is no longer an error to include custom plots in a study without assays or samples data (reported by Joe LoGrasso). Also relaxed the validation requirement for custom plots so that the study can contain assays data but not corresponding samples data

• Bug fix: Custom plotting functions cannot have the same name as any of the functions defined in the base package. This error is now caught early with addPlots() (reported by Anastasia Galperina)

1.6.3

• The release tarball includes version 1.3.4 of the web app

1.6.2

• The release tarball includes version 1.3.3 of the web app

1.6.1

• The release tarball includes version 1.3.2 of the web app

• New plotType of "multiTest". Include this when adding a custom plot with addPlots() to have the app pass the results tables for all testIDs for a given modelID (implemented by Marco Curado in PR #6)

• Bug fix: The documentation states that the assays table must only contain numeric columns. However, if a user added a data frame with non-numeric columns, no warning or error occurred. Now addAssays() will throw an error if it detects any non-numeric columns (reported by Anastasia Galperina in WebApp Issue #57)

1.5.2

• The release tarball includes version 1.3.1 of the web app

1.5.1

• The release tarball includes version 1.2.1 of the web app

• Both plotStudy() and getPlottingData() gained a new argument testID. If supplied, the R object passed to your custom plotting function will include the element results that contains the rows of the results table for that testID for the provided featureID(s). The app always passes the testID when calling plotStudy(). If your plotting function doesn't need the information in the results table, it will continue to work as before (implemented by Marco Curado in PR #4)

1.4.3

• Bug fix: Prevent a single missing value in an ID column that is required to be unique (reported by Marco Rocha Curado)

• Report the error message from R CMD build as a warning if exportStudy() fails to create a tarball for a study package

• Add the argument reset to addOverlaps(). You would only potentially need this if you are pre-calculating the annotation term overlaps prior to exporting the study

• Skip tests that fail only on CRAN Linux and macOS machines. The tests will continue to run on GitHub Actions

1.4.2

• Prepare for CRAN submission

1.4.1

• The release tarball includes version 1.1.9 of the web app

• Optional support for model metadata via addModels() and getModels(). Previously you could only add a single string to describe each modelID, which would be displayed in the app as a tooltip. Now you also have the option to provide a list with arbitrary metadata. The tooltip is derived from the list element description (if it exists)

1.3.1

• New function importStudy() to import an installed study package into R as an onStudy object. This is intended to be used to edit a study when you don't have access to the original data and code that created it

• Optional support for test metadata via addTests() and getTests(). Previously you could only add a single string to describe each testID, which would be displayed in the app as a tooltip. Now you also have the option to provide a list with arbitrary metadata. The tooltip is derived from the list element description (if it exists)

1.2.1

• The release tarball includes version 1.1.8 of the web app

• New function removeStudy() to remove an installed study package

• New argument studyMeta for createStudy(). You can add metadata to describe your study. See ?createStudy and the User's Guide for more details.

• New arguments maintainer and maintainerEmail for createStudy() to make it easier for others to know who to contact for questions about your study

• listStudies() now returns all the fields in DESCRIPTION for each study package

• Fixed minor bug in listStudies(). It couldn't find study packages in directories not included in .libPaths(). This likely only affected the unit tests.

1.1.7

• The release tarball includes version 1.1.7 of the web app

• Added support for linkouts in metaFeatures table. See ?addMetaFeaturesLinkouts for details. These linkouts will be displayed as favicons in the metaFeatures table in a future release of the app.

• The "add" functions have a new argument, reset. If reset = TRUE, then the existing data is removed prior to adding the new data. The default continues to be to add to or modify any existing data.

1.1.6

• The release tarball includes version 1.1.6 of the web app

• Package functions are now "data.table aware". This is an internal change only. The output is unaffected, and functions are potentially faster.

1.1.5

• The release tarball includes version 1.1.5 of the web app

• Fix bug in getResultsIntersection() where adding additional filters resulted in more results when notTests were specified, instead of fewer (reported by Terry Ernst, Brett Engelmann, and Wendy Waegell)

1.1.4

• The release tarball includes version 1.1.3 of the web app

1.1.3

• The release tarball includes version 1.1.2 of the web app

• Bug fix: exportStudy() can now export a study as a package tarball to a path that contains spaces or quotes (reported by Naim Mahi and Brett Engelmann)

• Bug fix: Study packages will now use custom description if supplied to createStudy(). Hover over the study name in the app to see the custom package description (reported by Paul Nordlund and Brett Engelmann)

1.1.2

• The release tarball includes version 1.1.1 of the web app

• Bug fix: installApp() now properly searches for the installed OmicNavigator package. It usually worked before, but now it should always work.

1.1.1

• The release tarball includes version 1.1.0 of the web app

1.1.0

• New function installApp() to download the web app after installing the R package

• Support for tibble and data.table input. For consistency, they will be be automatically converted to pure data frame objects internally.

• Bug fix: exportStudy() now properly overwrites an existing tarball when the argument path is used (reported by Brett Engelmann)

• Bug fix: getResultsIntersection() now properly returns the filtered table in the original order from getResultsTable() (reported by Paul Nordlund)

1.0.0

• The release tarball includes version 1.0.0 of the web app
• UpSet plots now display a maximum of 30 intersections (previously was 40)
• UpSet plots now no longer display empty intersections

0.24.1

• The release tarball includes version 0.3.8 of the web app
• Report versions of R package and app when first attached
• Send warning if the version of the app is not the version pinned to the installed version of the R package

0.24.0

• Breaking change: plotStudy() and getPlottingData() now accept multiple featureIDs as input in order to visualize multiple feature in a single plot. The object returned by getPlottingData() is now a list of three data frames: assays, samples, and features. Thus you can annotate your plots with any feature metadata. You will need to update your custom plotting functions to accept one argument (you can name it whatever you like). Also, when adding plots with addPlots(), specify the plotType as "singleFeature" or "multipleFeature" to accept a single or multiple featureIDs, respectively. The app currently only supports singleFeature custom plots, but will soon support multiFeature plots as well. Study packages must be rebuilt with OmicNavigator 0.24.0.

• Fix bug in getResultsUpset() that failed when using the absolute value filters (|<|, |>|)

• getResultsUpset() now throws an error when there are no features remaining for plotting after the filters are applied

0.23.1

• The release tarball includes version 0.3.7 of the web app

0.23.0

• The release tarball includes version 0.3.6 of the web app

• Use faviconPlease to find URLs to favicons for table linkouts

• Optimize getResultsUpset() for speed. Input remains unchanged. The plotting data is now returned invisibly. The default font size for the UpSet plot was increased.

• Apply MIT license

• Fix bug in getResultsIntersection() when a modelID has no features table. The "Set_Membership" column was returned in the first column instead of after the featureID column (reported by Joe Dalen and Paul Nordlund)

• Fix bug in getResultsUpset() when the results tables have differing number of features

0.22.5

• The release tarball includes version 0.3.5.3 of the web app

0.22.4

• The release tarball includes version 0.3.5.2 of the web app

0.22.3

• The release tarball includes version 0.3.5.1 of the web app

0.22.2

• The release tarball includes version 0.3.5 of the web app

0.22.1

• The release tarball includes version 0.3.4 of the web app

0.22.0

• New function getFavicons() to obtain URLs to favicons to display table linkouts. Currently just a wrapper around Google's favicon service, but in the future will be more sophisticated.

0.21.8

• The release tarball includes version 0.3.3 of the web app

• Improved support for numeric-looking featureIDs, e.g. 1234 or 0001

0.21.7

• The release tarball includes version 0.3.2.1 of the web app

0.21.6

• The release tarball includes version 0.3.2 of the web app

0.21.5

• The release tarball includes version 0.3.1 of the web app

• User's Guide:

  • Document minimal valid study
  • New section: Mapping between data elements and app features
  • Add linkouts to results and enrichments tables

• Moved UpSetR to a suggested dependency. This allows for a light-weight installation when you only need to create a study and not run the app. As an example, a continuous integration job that builds a study package tarball.

• Relax some of the validation requirements. Not all the featureIDs in the results tables must be in the features or metaFeatures tables.

0.21.4

• If a study has no features table for a modelID, a study can still have linkouts to external resources in the results table, as long as the linkouts only refer to the featureID column.

• validateStudy() now throws an error if the results and features table for a given modelID share any column names in addition to the featureID column. In other words, it validates that the only column name in common between the two tables is the first column.

0.21.3

• The release tarball includes version 0.2.8 of the web app

• validateStudy() now throws an error if there are any featureIDs in the metaFeatures table that are not included in the features table (reported by Paul Nordlund)

0.21.2

• The release tarball includes version 0.2.7 of the web app

0.21.1

• The release tarball includes version 0.2.6.1 of the web app

0.21.0

• Support for linkouts to external resources in results and enrichments tables

• New function getPackageVersion() for the app to conveniently query the current installed version of the R package

0.20.1

• The release tarball includes version 0.2.5 of the web app

• validateStudy() now throws a warning if the results tables for the tests of a model have no common columns. The lack of common columns will disable the UpSet filtering in the app for that model.

0.20.0

Breaking change

• exportStudy() - The argument type has changed. Studies can no longer be exported as RDS (type = "rds") or text files (type = "text"). This is because these were no longer able to capture all of the information that can potentially be included in a study package (e.g. custom plotting functions, report files). Instead, the default is now the new option "tarball". This will export the study package as a source package tarball, which is ready to be installed directly with install.packages(). The option "package" remains; it exports the study as a package directory.

New feature

• The "get" functions have a new argument quiet. Setting quiet = TRUE will suppress any messages, such as reporting unavailable data or the use of the "default" data.

Miscellaneous

• Improved the messages from installStudy() and exportStudy()

• validateStudy() now performs more in-depth check to validate that the featureIDs are consistent between the results, features, and assays tables

0.19.0

• Most package functions now consistently return empty data structures (e.g. list()) when a query requests data that is unavailable. Previously the functions would throw an error if the requested data was unavailable. There is a new section in the API vignette documenting this behavior for the functions called by the app.

• It is now possible to export a study that only contains a single results table.

0.18.2

• The release tarball includes version 0.2.4.1 of the web app

0.18.1

• The release tarball includes version 0.2.4 of the web app

0.18.0

Breaking change

• Changed name of app and R package from OmicAnalyzer to OmicNavigator. This breaks all previously installed study packages. Re-run your scripts to re-install the study packages. Also note that the default study package prefix has changed from "OAstudy" to "ONstudy".

Other changes

• The release tarball includes version 0.2.3 of the web app

0.17.0

Breaking change

• The input to addTests() is now a named list, similar to addModels(). You will need to update your code and re-install any existing OmicNavigator study packages.

Other updates

• New package option OmicNavigator.prefix to control the prefix used to label OmicNavigator study packages. The default is still "OAstudy". Run ?OmicNavigator for more information on OmicNavigator package options.

0.16.2

• The release tarball includes version 0.2.2 of the web app

0.16.1

• The release tarball includes version 0.2.1 of the web app

0.16.0

• New User's Guide and API vignettes created with Sweave

• Add summary() method for OmicNavigator study objects (class onStudy)

• Bugfix: listStudies() now works if its argument libraries is pointed to a specific directory

0.15.0

• The release tarball includes version 0.1.9.1 of the web app

• Remove the argument overwrite for the add functions, e.g. addSamples(). Instead subsequent calls to the same add function will update the existing data using the rules of utils::modifyList().

• addMetaFeatures() now automatically converts all columns to character. It throws a warning if it detects any non-character columns.

• getMetaFeatures() and getMetaFeaturesTable() always return the columns of the features table as character strings, even if they appear numeric.

• Support the option to manually calculate pairwise overlaps with addOverlaps() prior to installing or exporting the study package.

0.14.1

• The release tarball includes version 0.1.8 of the web app

0.14.0

• Support for linking to external analysis report files (addReports(), getReports(), getReportLink()). Accepts a URL or a path to file.

• New function validateStudy() to validate a study. It is automatically run prior to exporting with exportStudy() (controlled by the new argument requireValid). It can also be run directly.

• createStudy() now checks that the arguments name, description, and version are valid.

• exportStudy() no longer exports empty directories for unused elements of the OmicNavigator study object.

• Bug fix: getMetaFeaturesTable() now properly returns a data frame even if it only contains one column.

0.13.3

• Bug fix: Preserve input order for results table. Due to the merge with the features table, getResultsTable() was changing the original row order. Bug identified by Brett Engelmann.

0.13.2

• The release tarball includes version 0.1.7 of the web app

0.13.1

• addFeatures() now automatically converts all columns to character. It throws a warning if it detects any non-character columns.

• getFeatures() and getResultsTable() always return the columns of the features table as character strings, even if they appear numeric.

0.13.0

This release includes substantial internal changes. The study data is now exported as plaintext files instead of as an SQLite file. There are no changes to the API, so no changes need to be made to R scripts or the JavaScript frontend. However, since the storage mechanism has changed, all existing OmicNavigator studies need to be reinstalled in order to be compatible with this version. Furthermore, the dependencies have changed, so you may have to re-run remotes::install_deps().

0.12.1

• The release tarball includes version 0.1.6 of the web app

0.12.0

• The release tarball includes version 0.1.5 of the web app

• getEnrichmentsUpset() has a new argument tests, which restricts the UpSet plot to only include the desired tests (#1, Justin Moore)

0.11.0

• The release tarball includes version 0.1.4 of the web app

• If startApp() is unable to run because the package was installed without the bundled web app, provide the URL for the releases page to download the tarball. Also offer to open the page in the browser.

0.10.0

• More documentation of function arguments
• New function getMetaFeatures()
• New function getMetaFeaturesTable()

0.9.3

• The release tarball includes version 0.1.3 of the web app

0.9.2

• Fix bug in getResultsIntersection() introduced in commit ff1ac89 and released in version 0.7.0

• The release tarball includes version 0.1.2 of the web app

0.9.1

• The release tarball includes version 0.1.1 of the web app

0.9.0

• The release tarball includes version 0.1.0 of the web app. Run startApp() to run it locally.

• New function getUpsetCols() to get the columns common across all tests of a model, and thus are available for filtering with UpSet.

• getBarcodeData() now returns data in decreasing order of the statistic column (requested by Paul Nordlund)

• addBarcodes() now has an additional optional field featureDisplay. This can be set to any column of the features table, and that feature metadata variable will be used to label the barcode plot (requested by Paul Nordlund). If featureDisplay is not set, it will be automatically set to the feature metadata variable used in the enrichment analysis. getBarcodeData() now returns three feature-related columns:

  • featureID - The unique feature variable used in the inference results table
  • featureEnrichment - The feature variable used to perform the enrichment analysis with the given annotation database
  • featureDisplay - The feature variable to use to label the barcode plot on hover

  Note that these will all be identical in the simple case where the study featureID is used for the enrichment analysis.

0.8.0

• getBarcodeData() now returns both the study featureID (in the column featureID) and the featureID used by the annotation database (in the column featureDisplay). The former is needed to pass to plotStudy() to generate any custom plots. The latter is needed to display when hovering over the barcode plot (reported by Paul Nordlund).

• Fix bug in plotStudy() related to detaching package namespaces. When a custom plot specified more than one package dependency, the last package listed would always be detached from the search path (even if it shouldn't have been since it was already attached). Furthermore, the other packages would never be detached (even if they should have been since they were not attached beforehand). The bug was caused by calling detach() with on.exit(), which used the latest value of the variable.

0.7.0

• New function getPlottingData() to return the data required by the first argument of the custom plotting functions.

• getResultsIntersection() positions the column Set_Membership between the feature metadata variable columns and the results columns

• Study packages that includes plots using base graphics now import the graphics package

• Fix bug when querying model-specific barcode metadata. Affected both getBarcodes() and getBarcodeData() (reported by Paul Nordlund)

• Remove warning from graphics::par() by only having plotStudy() reset the graphing parameters if they are changed by the custom plotting function

0.6.0

• New function startApp() to start the app running on local machine

• Fix bug in getResultsIntersection() so that it returns the feature metadata columns that are included in getResultsTable()

• Fix bug in getResults() that returned columns of NA for columns specific to other tests (only affected study packages, not onStudy objects)

0.5.1

• Fix bug in getPlots() so that it returns model-specific custom plots from the database of installed study package

0.5.0

• Changed <= and >= to < and >, respectively, to match app UI. Affects the functions getResultsIntersection(), getEnrichmentsIntersection(), getResultsUpset(), and getEnrichmentsUpset().

• Support customization of barcode plots:

  • addBarcodes()
  • getBarcodes()
  • getBarcodeData()

• getAnnotations()

• Changed the input argument of plotStudy() from feature to featureID

• Changed the argument name of custom plotting functions from feature to featureID

0.4.0

• getResultsIntersection()
• getEnrichmentsIntersection()
• getResultsUpset()
• getEnrichmentsUpset()