Changes in version 2.99.0
New features
- The pcaplot() function now provides a clever default for the
intgroup parameter, if some content (as it should) is provided in
the colData slot of the main input object
Other notes
- The transition to the functions available in the mosdef Bioconductor
is complete, with the original functions now being deprecated. This
applies to topGOtable() (now replaced by mosdef::run_topGO())
- The gene plot widgets now also use the gene_plot() function from
mosdef, instead of the previous undocumented internal function
- The Roxygen-based documentation now supports markdown. No visible
changes should appear to the user, as the content should have stayed
fairly the same
- Although no visible changes for the end user are expected, the
incoming major version bump will reflect the change in the
dependency graph, ensuring that this is noticed at least at the
version numbering level
Changes in version 2.22.0
Other notes
- get_annotation_orgdb() gains an additional argument,
key_for_genenames, which defaults to "SYMBOL". This should not
change the behavior of the function, if not specified, but
accommodates for the use of annotation packages where the
information has been encoded differently (e.g. org.Sc.sgd.db where
the info is contained in the "ORF" column)
Bug fixes
- pcaplot correctly returns the values for the percent of explained
variance, which were correctly displayed on the plot but not stored
as they should in the attribute slot
Changes in version 2.20.0
Other notes
- the tables in the PCA2GO tab panel can be compacted only if they are
computed via the pca2go function (offline) - at runtime,
limmaquickpca2go is used and no compaction is required
- if an annotation is provided with a column gene_id, these values are
actually overwriting the rownames (makes the object more robust with
respect to its provenance)
Changes in version 2.16.0
Other notes
- Replaced dependency from d3heatmap with the functionality of
heatmaply
Changes in version 2.12.0
Bug fixes
- Fixed an error in the initialization of the app due to a new
behavior introduced by shinyAce in version >= 0.4.0
- topGOtable does not generate rows with NAs if providing a too high
number for the categories to report
Other notes
- The type of the columns in the data.frame returned by topGOtable are
now correctly referring to the type they contain - e.g. the p values
are now stored as numeric values
- Citation now refers to the published manuscript -
https://doi.org/10.1186/s12859-019-2879-1
Changes in version 2.10.0
New features
- Added extra parameters to topGOtable to offer more control on the
method used, and the option to correct the p-values for multiple
testing (via the Benjamini-Yekutieli procedure)
- pca2go has now an option to return (early) a list with vectors of
genes with high loadings
- Better preview of the uploaded data with modal dialog windows
triggered by buttons which appear once corresponding inputs are
available
- Improved notification system: in addition to the progress bar, info
that all input is correctly specified, or suggest optional
annotation loading
- Added flexibility to select separator for each of the uploadable
files
- The pairwise correlation plots can now use logarithmic scale in the
axes, use smaller subsets of the data for quicker inspection, and
resizes the correlation info proportionally to its intensity
- The sample to sample heatmap supports additionally manhattan and
correlation-based distances
- There is a new vignette with a detailed quick start, "Up and running
with pcaExplorer", specifying how the workflow with pcaExplorer can
look like, demonstrated on the airway dataset
- In the Instructions panel, we added buttons to access the fully
rendered documentation, either local or online if e.g. deployed to a
server. Related to this, pcaExplorer has a new parameter, runLocal,
to control this behavior
- An additional parameter, annopkg, has been added to pca2go() to
override the behavior with the organism parameter (this is useful
when the name of the annotation package is not conform to the
classical org.Xx.eg.db, e.g. for Arabidopsis Thaliana); a detailed
use case has been added in the main vignette
Other notes
- The computing of the required objects now requires the explicit
action on the dedicated button, and the tooltip informs the user on
what steps are taken (including normalization)
- An information box has been added to provide detailed information on
the required input formats
- Added notification to specify how to install the airway package for
demonstration purposes if not already available
- Added startup message upon loading the package
- The content in the Instructions tab is now contained in collapsible
elements
- The file formats accepted by pcaExplorer are now specified both in
the vignette text, as well as in the app at runtime
- The content of the Instructions tab is now more compact, containing
the rendered "Up and running with pcaExplorer" vignette. The full
vignettes can be accessed via buttons in the same panel
- Added instructions to install phantomJS via the webshot package -
would raise an error when previewing the report
Changes in version 2.8.0
New features
- Added a NEWS.md file to track changes to the package
- PCA plots now are correctly generated with fixed coordinates
- Introduced use of conditionalPanels for better handling of errors in
the app tabs
- Added possibility to use different transformations, also reflected
in the change of one of the main arguments (previously rlt, now dst,
i.e. DESeqTransform): rlog, vst, shifted log, ... The transformation
type is tracked in the reactive values.
- More modular loading of data, by splitting generation of dds and dst
- pca2go is now also picking values from the input widgets
Other notes
- Built project website via pkgdown, with customized reference
structure
- Correctly adding the resources to shinyBS, loaded via .onLoad, and
also better placement for bstooltips
- Editor options start collapsed in the Report Editor tab
- Vignette and template report are updated to reflect the new
parameter names
- Uniformed style for ggplot2 plots
- Better tooltip placement in the main page
- Replaced print calls with more appropriate messages
- Displaying user returned messages in long (plotting) operations
Bug fixes
- Fixed behavior of rendering inline the content of the report - did
not work properly for server deployed instances
Changes in version 2.6.0
New features
- Automatically computing size factors where required
- Added progress indication when compiling the report
Bug fixes
- Fixed after changes in threejs package
- Edited dropdown menu to remove unused green badge
- Menus start expanded on the side, again
- theme_bw applied when needed, corrected previous behavior
Other notes
- Updated citation infos
- Slight difference in handling validate/need errors
Changes in version 2.2.0
New features
- Added Demo data, loadable via demo button
Bug fixes
- Plots work now without cutting out points when zooming in
Other notes
- Saved reactive values are now exported to dedicate environments
(instead of assigning to global)
Changes in version 1.99.0
Other notes
- Reflecting the major feature added, will trigger a major version
number bump. Welcome soon, pcaExplorer 2.0.0!
Changes in version 1.1.5
New features
- Automated report generation - template available + editor in the app
tab for advance user customization
- Support for state saving, in the global environment as well as with
binary data
- All plots generated can be now exported with the dedicated button
- Added confidence ellipse for PCA plot
- Added 3d pca plot
- Added functions to automatically retrieve the annotation in format
ready to use for the app
- Added profile explorer function, for plotting behaviour across all
samples for subset of genes
- Added distribution plots
- Added pairwise correlation plot
- Added table to enhance readability of the gene finder plot, also by
annotating sample names
Bug fixes
- Minor typos fixed in the tabs
- Added option row.names to read.delim for allowing row names when
uploading the data
Other notes
- Added extra info in the about section
- Instructions and vignette rewritten to reflect new design of the app
Changes in version 1.1.3
Bug fixes
- Remove y axis limits to gene boxplots
- Fixed: correct labels and colors assignements for genespca
Changes in version 1.0.0
Other notes
- Released in Bioconductor 3.3
Changes in version 0.99.1
Other notes
- Changed format of the NEWS file
Changes in version 0.99.0
Other notes
- Ready for submission to Bioconductor
Changes in version 0.9.0
Other notes
- Added TravisCI integration for both branches
- Added appveyor integration - plus badges in the README.md
- Code cleanup
- Added screenshots for the vignette
- Removed some lengthy tests
Changes in version 0.8.0
New features
- Selection of identifier type available in pca2go
Bug fixes
- Couple of layout fixes
Other notes
- MIT license
- Added TravisCI integration
- Added codecov integration
- Enhanced documentation
Changes in version 0.7.0
New features
- Vignette full draft done
Changes in version 0.6.4
Other notes
- Updated NEWS file
Changes in version 0.6.3
New features
- About and Instructions done by now
- Added some missing details on the documentations
Changes in version 0.6.2
Other notes
- Corrected wordings for (cor)relations of principal components with
covariates
- Added a couple of checks if correct objects are provided
Changes in version 0.6.1
New features
- Added function to remove selected samples suspected to be deemed as
outliers, in order to see the effect of clustering on the good ones
Changes in version 0.6.0
Other notes
- Documentation completed
- Examples fully working, cleaned up further a little more.
Changes in version 0.5.0
Other notes
- Further steps in direction of R CMD check
Changes in version 0.4.0
New features
- Added pca2go live functionality
Changes in version 0.3.0
New features
- Added color palette to choose, and dependent on the samples and
factors available/selected
Changes in version 0.2.0
New features
- Multifactorial exploration completed and adaptable to each dataset
Changes in version 0.1.0
New features
- Restyling and (re)packaging mostly completed