NEWS

---

Cardinal 3.7.3

BUG FIXES

• Fix plot() and image() not always respecting dimnames

Cardinal 3.7.2

BUG FIXES

• Bug fixes for 'plot()' on spectra with queued processing

Cardinal 3.7.1

NEW FEATURES

• Update 'spectrapply()' to support 3 index arrays
• Update 'plot()' to support 2 domains (e.g., for ion mobility)
• Add plotting methods for 'XDataFrame' and 'PositionDataFrame'

BUG FIXES

• Fix default 'tolerance' in 'pixels()'

Cardinal 3.6.3

BUG FIXES

• Bug fixes for 'meansTest()' when random effects are specified

Cardinal 3.6.2

BUG FIXES

• Version bump for 'matter' 2.6.2 bugfixes

Cardinal 3.6.1

SIGNIFICANT USER-VISIBLE CHANGES

• Add 'mass.range' and tolerance' arguments to 'bin()'

BUG FIXES

• Fix 'readImzML' error if imzML fails conversion to 'ImzMeta'

Cardinal 3.5.6

SIGNIFICANT USER-VISIBLE CHANGES

• Add optional 'run' argument to 'slice()'
• Add optional 'plotly' support for all plotting methods

Cardinal 3.5.5

BUG FIXES

• Fix bug in 'selectROI()' region plot updates

Cardinal 3.5.4

NEW FEATURES

• Re-add support for 3D coordinates and 'image3D()'

SIGNIFICANT USER-VISIBLE CHANGES

• Export 'vizi_style()' and 'vizi_engine()' functions
• Add 'check' argument to 'readMSIData()' for uuid+checksum

BUG FIXES

• Fix bug in plotting PLS/OPLS coefficients
• Fix removing position columns with 'coord()<-'

Cardinal 3.5.3

NEW FEATURES

• Add support for multiple instance learning for 'PLS()' and 'spatialShrunkenCentroids()' with 'bags' argument
• Add 'estimateReferenceMz()' for more easily estimating profile m/z-values from 'MSImagingArrays'

BUG FIXES

• Make sure 'bin()' still respects 'resolution' when 'ref' is specified (in which case the range is taken from 'ref')
• Fix 'crossValidate()' for multiple instance learning

Cardinal 3.5.2

BUG FIXES

• Fix passing 'tolerance' in 'peakProcess()' when not needed
• Fix bugs in 'selectROI()' not updating the plot
• Fix bugs in 'selectROI()' selecting wrong pixels
• Make sure 'peakAlign()' produces similar results when re-aligning peaks with the same tolerance

Cardinal 3.5.1

NEW FEATURES

• Ground-up rewrite to take advantage of matter v2.5 features
• New class 'SpectraArrays' for arrays of spectra
• New class 'SpectralImagingData' for spectral imaging data
• New class 'SpectralImagingArrays' for raw spectra
• New class 'SpectralImagingExperiment' for centroided spectra
• New class 'MSImagingArrays' for raw mass spectra
• Updated class 'MSImagingExperiment'
• Updated class 'XDataFrame'
• Updated classes 'PositionDataFrame' and 'MassDataFrame'
• New apply method 'spectrapply()'
• New processing method 'recalibrate()'
• New processing method 'bin()'
• New processing method 'peakProcess()'
• New classes 'SpatialResults' and 'ResultsList'
• Updated spatial methods 'findNeighbors()' and 'spatialWeights()'
• Updated spatial methods 'colocalized()'
• Updated projection methods 'PCA()' and 'spatialFastmap()'
• New projection method 'NMF()'
• Updated stats methods 'PLS()' and 'OPLS()'
• Updated stats method 'spatialKMeans()'
• Updated stats method 'spatialShrunkenCentroids()'
• Updated stats method 'spatialDGMM()'
• Improved visualization methods 'plot()' and 'image()'

SIGNIFICANT USER-VISIBLE CHANGES

• Deprecated 'smoothSignal()' -- use 'smooth()'
• Deprecated 'mzBin()' -- use 'bin()'
• Deprecated 'mzAlign()' -- use 'recalibrate()'
• Deprecated 'mzFilter()' -- use 'subsetFeatures()'
• Deprecated 'peakFilter()' -- use 'subsetFeatures()'
• Deprecated 'aggregate()' -- use 'summarizeFeatures()'
• Deprecated 'featureApply()' -- use 'summarizeFeatures()'
• Deprecated 'pixelApply()' -- use 'summarizePixels()'

Cardinal 3.4.3 (2023-11-22)

BUG FIXES

• Fixed default calculation of reference peaks in 'peakAlign()'

Cardinal 3.4.2 (2023-11-16)

BUG FIXES

• Fixed error in 'readImzML()' if spectrum representation is missing
• Fixed bug in 'writeImzML()' causing overlapping offsets

Cardinal 3.4.1 (2023-10-25)

BUG FIXES

• Fixed bug in 'writeImzML()' causing malformed cvParam tag

Cardinal 3.3.5 (2023-10-19)

BUG FIXES

• Allow 'guess.max=Inf' in 'readImzML()'

Cardinal 3.3.4 (2023-10-19)

SIGNIFICANT USER-VISIBLE CHANGES

• Bin peaks when importing centroid spectra with 'readImzML()'
• Replaced all functions from deprecated 'sp' package

Cardinal 3.3.3

BUG FIXES

• Fixed I/O bugs introduced by matter v2.3.13 changes

Cardinal 3.3.2

BUG FIXES

• Fixed I/O bugs introduced by matter v2.3.11 changes
• Other I/O bugs fixed by matter v2.3.13 changes

Cardinal 3.3.1

BUG FIXES

• Merged 3.2.1 fixes to resolve R CMD check warnings

Cardinal 3.2.1

BUG FIXES

• Cleaned up escaped LaTeX specials in documentation
• Fixed 'sprintf()' => 'snprintf()' warning in C code

Cardinal 3.0.1 (2022-11-14)

SIGNIFICANT USER-VISIBLE CHANGES

• Overwriting existing MSI files is now a warning instead of an error

BUG FIXES

• Fixed issue in 'peakAlign()' reference m/z's being sort and unique

Cardinal 2.99.1 (2022-10-31)

SIGNIFICANT USER-VISIBLE CHANGES

• Updated vignettes for Cardinal 3
• Widened default m/z 'tolerance' for sparse spectra
• Switched to linear interpolation for sparse spectra

Cardinal 2.99.0 (2022-10-26)

SIGNIFICANT USER-VISIBLE CHANGES

• Updated out-of-memory backend to Matter 2.0
• Removed support for legacy classes and methods

Cardinal 2.11.3

BUG FIXES

• Fix strange behavior from random number generation in R >= 4.1.1

Cardinal 2.11.2

BUG FIXES

• Fix reference naming scheme for binning and alignment methods

Cardinal 2.11.1

BUG FIXES

• Use as(x, 'DFrame') instead of as(x, 'DataFrame')
• Fix logical length > 1 error in 'segmentationTest()'

Cardinal 2.7.2 (2020-10-21)

SIGNIFICANT USER-VISIBLE CHANGES

• For 'mzAlign()', the 'ref' parameter now expects a vector of reference m/z-values rather than a complete spectrum

Cardinal 2.7.1

BUG FIXES

• Fixed issue where 'spatialDGMM()' would sometimes fail for features with singular segmentations
• Suppressed warnings on 'Mclust()' initialization to 'spatialDGMM()' caused by R 4.0 changes
• Fixed pixel/feature mapping in 'spatialDGMM()' metadata

Cardinal 2.5.12

BUG FIXES

• Drawing a region-of-interest using 'selectROI()' should now update the plot properly in RStudio devices
• Fixed issues with automatically guessing a reasonable mass tolerance for certain pre-processing methods
• In 'mzBin()', the previous value of 'centroided()' from the original dataset is now preserved after binning

Cardinal 2.5.11

BUG FIXES

• Fixed bug in 'spatialShrunkenCentroids()' that produced in NaNs when discriminant scores were very large
• Fixed bug in 'spatialFastmap()' where subsetting produced vectors instead of matrices due to omitting 'drop=FALSE'

Cardinal 2.5.10

NEW FEATURES

• Added 'topFeatures()' method for 'spatialKMeans()'
• Added coercion to 'DataFrame' from 'MSImagingExperiment'

SIGNIFICANT USER-VISIBLE CHANGES

• Deprecated legacy classes (MSImageSet, etc.): class definitions will remain for supporting datasets from CardinalWorkflows, but methods operating on them will be defunct in BioC 3.12

Cardinal 2.5.9

NEW FEATURES

• Added 'aggregate()' method for imaging experiments including 'summarizePixels()' and 'summarizeFeatures()'
• Added 'subset()' method for imaging experiments including 'subsetPixels()' and 'subsetFeatures()'

SIGNIFICANT USER-VISIBLE CHANGES

• Deprecated 'dplyr' verbs in favor of the above functions; this is to remove the (rather large) dependency on the tidyverse for a relatively small functionality

BUG FIXES

• Fix bug in 'spatialDGMM()' printing caused by a change in default.stringsAsFactors() == FALSE in R 4.0

Cardinal 2.5.8

NEW FEATURES

• Automatic estimation of mass resolution will now work for 'processed' imzML with centroid spectra
• New getter/setter options for Cardinal options such as 'getCardinalBPPARAM()' and 'setCardinalBPPARAM()'

SIGNIFICANT USER-VISIBLE CHANGES

• Default BPPARAM backend is now set to 'SerialParam()'; use 'setCardinalBPPARAM()' to change the backend
• Expose '.view' argument of 'matter::chunk_apply()' in 'pixelApply()', 'featureApply()', and 'spatialApply()'
• Previously-deprecated functions 'generateSpectrum()' and 'generateImage()' are now defunct
• Removed defunct functions 'Binmat()' and 'topLabels()'

BUG FIXES

• Fix large intensity text cutoffs in 'image()' colorkey

Cardinal 2.5.7

BUG FIXES

• Fix bug when using 'rbind()' or 'cbind()' on 'MassDataFrame' and 'PositionDataFrame'

Cardinal 2.5.6

BUG FIXES

• Fix bug when assigning a dense matrix via iData()<- for an 'MSProcessedImagingExperiment' object

Cardinal 2.5.5

BUG FIXES

• Fix bug in 'show' method for 'SimpleImageList' caused by class(matrix) -> c("matrix", "array")

Cardinal 2.5.4

BUG FIXES

• Fix bugs in legacy classes caused by a change in default.stringsAsFactors() == FALSE in R 4.0

Cardinal 2.5.3

SIGNIFICANT USER-VISIBLE CHANGES

• The 'resolution' argument in all methods has been redefined to always mean **full bin widt for both "mz" and "ppm" units

Cardinal 2.5.2

SIGNIFICANT USER-VISIBLE CHANGES

• The 'pixelApply()', 'featureApply()', and 'spatialApply()' methods now internally use 'matter::chunk_apply()'

Cardinal 2.5.1

BUG FIXES

• Fixed bug in 'mzBin()' binning spectra incorrectly
• Fixed bug in contrast enhancement with missing intensities

Cardinal 2.3.18 (2019-10-27)

SIGNIFICANT USER-VISIBLE CHANGES

• Processing in 'crossValidate()' now allows processing unprocessed data by performing peak-picking on the mean spectra of the training sets

BUG FIXES

• Fixed some errors in user messages during peak processing

Cardinal 2.3.17 (2019-10-25)

SIGNIFICANT USER-VISIBLE CHANGES

• Default for 'peakBin()' argument 'type' is now "area"
• In 'peakBin()', peak boundaries should be calculated more accurately now, and general speed improvements
• In 'peakAlign()', peak centers are now calculated as weighted average mass rather than the highest point

Cardinal 2.3.16 (2019-10-14)

NEW FEATURES

• New class 'ImagingSummary' with sub-classes including 'SparseImagingSummary' and 'MSImagingSummary' with appropriate 'plot()' and 'image()' methods

SIGNIFICANT USER-VISIBLE CHANGES

• The 'summarize()' method for 'SparseImagingExperiment' now returns a 'SparseImagingSummary', to more closely reflect "tidy" data principles by returning an object of a similar class; the previous behavior can be reproduced by specifying '.as="DataFrame"'

Cardinal 2.3.15 (2019-10-13)

NEW FEATURES

• For methods requiring 'resolution' or 'tolerance', the default arguments have been updated to automatically guess based on the data

Cardinal 2.3.14

NEW FEATURES

• Add spectraData() as an alias for 'imageData()' for 'MSImagingExperiment' sub-classes
• Formalize 'mzData()' and 'intensityData()' getters and setters for 'MSProcessedImagingExperiment'
• Add 'peaks()' and 'peakData()' methods for extracting peak matrices and/or peak information
• Add 'isCentroided()' method for guessing whether spectra are centroided (without using the @centroided slot)

SIGNIFICANT USER-VISIBLE CHANGES

• Allow 'NA' for @centroided slot for 'MSImagingExperiment'
• 'mzBin()' method now sets centroided = NA
• Update 'mzFilter()' with parameter defaults so that 'thresh.max = NA' and new arg 'rm.zero = TRUE'
• Log more pre-processing information (e.g., method name)

Cardinal 2.3.13

BUG FIXES

• Try using 'parent.frame(1)' instead of 'parent.frame(2)' to fix NSE methods when used in LHS of a maggritr pipe
• Fix weird 'iData()<-' missing argument 'i' bug

Cardinal 2.3.12

SIGNIFICANT USER-VISIBLE CHANGES

• Changed default 'peakPick()' method to 'mad'
• In 'peakPick()' method 'mad', change the default number of blocks to 1 (no adaptive smoothing)
• In 'peakPick()' method 'mad', update w/ new arguments w/ new defaults 'fun=median' and 'tform=diff'

BUG FIXES

• In 'peakPick()' methods 'simple' and 'adaptive', warn if kurtosis cannot be estimated and try to recover
• In 'normalize()' method 'reference', provide a warning if the reference value is 0 for a pixel

Cardinal 2.3.11

SIGNIFICANT USER-VISIBLE CHANGES

• Improved speed in 'spatialFastmap()'
• Improved speed in 'spatialShrunkenCentroids()'
• New dissimilarity metrics for 'spatialFastmap()' including a new default metric='average'

BUG FIXES

• Fix error in 'print()' for facet plots where lims=NULL

Cardinal 2.3.10

SIGNIFICANT USER-VISIBLE CHANGES

• Improved speed in 'spatialDGMM()', by moving spatial filtering of probabilities to C code, up to 10x faster
• Linesearch in 'spatialDGMM()' now uses 'optimize()' rather than 'optim()' -- results may differ slightly

Cardinal 2.3.9

NEW FEATURES

• Added 'Cardinal.history()' and 'Cardinal.version()'

SIGNIFICANT USER-VISIBLE CHANGES

• Removed under-used setter generic function definitions

BUG FIXES

• Cleaned up generics to reflect ProtGenerics >= 1.17.2

Cardinal 2.3.8

NEW FEATURES

• Added boxplot, histogram, and bar chart functionality to the 'plot()' method for 'XDataFrame'
• Added 'plot()' plotting for 'AnnotatedImageList'
• Added 'plot()' methods for 'SpatialDGMM', 'MeansTest', and 'SegmentationTest' result classes
• Added 'image()' method for 'MeansTest' result class

SIGNIFICANT USER-VISIBLE CHANGES

• Updated 'plot()' and 'image()' methods for 'SpatialDGMM', 'MeansTest', and 'SegmentationTest' result classes

BUG FIXES

• Various bug fixes in object printing and plot auto-layout

Cardinal 2.3.7

NEW FEATURES

• Added 'image()' plotting for 'AnnotatedImageList'

BUG FIXES

• Plotting with 'add=TRUE' now respects 'par('usr')' coordinates

Cardinal 2.3.6

NEW FEATURES

• Add 'AnnotatedImageList' class for list of 'AnnotatedImage' objects
• Add 'AnnotatedImagingExperiment' class for containing data for an optical imaging experiment (e.g., a microscopy experiments)
• Add 'image()' plotting for 'AnnotatedImagingExperiment'

SIGNIFICANT USER-VISIBLE CHANGES

• Redefine '@featureData' slot of a 'SparseImagingExperiment' to be a 'DataFrame' rather than requiring an 'XDataFrame'

BUG FIXES

• Respect 'layout' and 'byrow' passed through ... args to 'print()' method on facet plot objects

Cardinal 2.3.5

SIGNIFICANT USER-VISIBLE CHANGES

• Moved some S4 method definitions from 'ImagingExperiment' to 'SparseImagingExperiment' so that the former can be more flexible for a wider variety of imaging modalities

BUG FIXES

• Pass more ... args through to 'par()' in plotting functions

Cardinal 2.3.4

NEW FEATURES

• Added 'AnnotatedImage' class for optical images

Cardinal 2.3.3

SIGNIFICANT USER-VISIBLE CHANGES

• Improved facet plotting when 'add=TRUE'

BUG FIXES

• Better 'cex.axis' defaults and user setting for colorkeys

Cardinal 2.3.2

SIGNIFICANT USER-VISIBLE CHANGES

• Improved 'writeMSIData()' for 3D and non-gridded data

Cardinal 2.3.1

NEW FEATURES

• Output directly to imzML while processing with 'process()'

SIGNIFICANT USER-VISIBLE CHANGES

• Improved auto-layout for visualization with multiple runs
• Added 'parse.only' option to 'readImzML()' for parsing only

Cardinal 2.2.4

BUG FIXES

• Fix large external array offsets in 'writeImzML'

Cardinal 2.2.3

BUG FIXES

• Cleaned up some 'writeImzML' mapping validity issues

Cardinal 2.2.2

BUG FIXES

• Removed curly braces around UUID when writing imzML

Cardinal 2.2.1

BUG FIXES

• Fixed bug in plotting results where 'column' argument would get matched before the 'col' argument

Cardinal 2.1.30

BUG FIXES

• Fixed bug where 'spatialShrunkenCentroids' classification would change the user 'options(Cardinal.progress)'

Cardinal 2.1.29

BUG FIXES

• Coercing to 'SpatialShrunkenCentroids2' now drops empty classes for segmentations (as expected)

Cardinal 2.1.28

BUG FIXES

• Fixed 'topFeatures' method for 'SpatialShrunkenCentroids2' where 'statistic' was actually printing the 'centers'
• The 'collect' method for 'MSProcessedImagingExperiment' now preserves sparseness when pulling into memory

Cardinal 2.1.27

SIGNIFICANT USER-VISIBLE CHANGES

• Added 'mzFilter' as an alias for 'peakFilter' with more suitable defaults for non-peak-picked spectra

BUG FIXES

• Minor fixes to 'print' method for plots and images
• Minor fixes to margin padding for 'colorkey' in images

Cardinal 2.1.26

BUG FIXES

• Fixed 'print' method for plots and images to respect updating plotting parameters via '...' arguments

Cardinal 2.1.25

SIGNIFICANT USER-VISIBLE CHANGES

• Add 'run' argument to 'pixels' for 'MSImagingExperiment'
• Add 'run' argument to 'plot' for 'MSImagingExperiment'

BUG FIXES

• Fixed bug in 'ylab' with one-sided formulas in 'plot'
• Relaxed errors for out-of-range m/z values in 'features'
• Value range of 'colorkey' now obeys 'zlim' argument
• NULL values for plot limits no longer give errors

Cardinal 2.1.24

SIGNIFICANT USER-VISIBLE CHANGES

• Documented new 'options(Cardinal.dark=FALSE)' default

BUG FIXES

• Fixed linear subsetting of models using '[” for 'SparseImagingResult' objects
• Check length of 'classControl' in 'segmentationTest'

Cardinal 2.1.23

NEW FEATURES

• Added 'slice' for slicing imaging datasets (as a data cube)
• Added 'alpha.power' argument for 'image' methods

SIGNIFICANT USER-VISIBLE CHANGES

• Added documentation for options() under '?Cardinal'

Cardinal 2.1.22

NEW FEATURES

• Added new 'Cardinal 2: Statistical methods' vignette

Cardinal 2.1.21

NEW FEATURES

• Added 'image3D' methods for new classes

Cardinal 2.1.20

SIGNIFICANT USER-VISIBLE CHANGES

• Updated documentation and simulation examples

BUG FIXES

• Fixed bug in 'summary' for 'SpatialShrunkenCentroids2'

Cardinal 2.1.19

NEW FEATURES

• Added 'colocalized' method for colocalization
• Added 'colocalized' method for colocalization

Cardinal 2.1.18

SIGNIFICANT USER-VISIBLE CHANGES

• Updated 'Cardinal 2: User guide' vignette

BUG FIXES

• Fixed bug in 'simulateSpectrum' when n > 1

Cardinal 2.1.17

NEW FEATURES

• Added 'topFeatures' method for extracting top-ranked features from statistical analyses
• Added 'summary' methods for new results objects
• Added 'SummaryDataFrame' for printing result summaries

SIGNIFICANT USER-VISIBLE CHANGES

• Deprecated 'topLabels' method -> use 'topFeatures'

Cardinal 2.1.16

NEW FEATURES

• Added dplyr verbs for 'DataFrame' and "XDataFrame'

Cardinal 2.1.15

NEW FEATURES

• Added new 'PCA' method for 'SparseImagingExperiment'
• Added new 'PLS' method for 'SparseImagingExperiment'
• Added new 'OPLS' method for 'SparseImagingExperiment'

SIGNIFICANT USER-VISIBLE CHANGES

• The 'selectROI' method will now use the last plot if no additional plotting arguments are given
• Setting 'resolution' on 'MSProcessedImagingExperiment' will now update the m/z values binning scheme
• The 'select' and 'filter' methods now using integers as row/col IDs without the '.id' argument

BUG FIXES

• Fixed bug in 'OPLS' methods causing cross-validation to produce slightly optimistic results

Cardinal 2.1.14

NEW FEATURES

• New 'mzAlign' processing method for spectral alignment
• New 'mzBin' processing method for spectral binning
• New 'crossValidate' method that cleans up 'cvApply' output
• New normalization methods: 'rms' and 'reference'
• New baseline reduction method: 'locmin'
• New peak picking method: 'mad'
• New 'darkmode' and 'lightmode' plotting options
• Added 'cvApply' methods for new classes

SIGNIFICANT USER-VISIBLE CHANGES

• Image plotting now uses different 'colorkey' legend placed beside plot that no longer obscures the image
• All plotting now uses different 'strip' labels placed above plot that no longer obscures the plot area
• All plotting now accept hidden 'dark=TRUE' argument to switch to plotting in new "dark mode"
• Changed/updated presets for 'presetImageDef' which provides presets for 'simulateImage' function

Cardinal 2.1.13

SIGNIFICANT USER-VISIBLE CHANGES

• Added message when printing a 'SparseImagingExperiment' object without un-applied pre-processing steps

BUG FIXES

• Added C routine registration with "C_" prefix for .Call
• Cleaned up '.o' objects in /src created by accident

Cardinal 2.1.12

NEW FEATURES

• Added 'meansTest' method for linear model-based hypothesis tests of mean-summarized images
• Added 'segmentationTest' method for linear model-based hypothesis tests of spatially-segmented images

Cardinal 2.1.11

SIGNIFICANT USER-VISIBLE CHANGES

• Added option to set the probability regularization parameter (p0) to 'spatialDGMM' method
• Added option to initialize 'spatialDGMM' algorithm with either k-means or Gaussian mixture model

Cardinal 2.1.10

SIGNIFICANT USER-VISIBLE CHANGES

• Changed default colorscale for images to 'viridis'
• Updated 'simulateImage' presets to handle multiple runs

Cardinal 2.1.9

NEW FEATURES

• Added 'spatialDGMM' method for fitting feature-wise spatially-aware Dirichlet Gaussian mixture models
• Added 'predict' method for 'SpatialShrunkenCentroids2'

BUG FIXES

• Fixed 'spatialShrunkenCentroids' classification methods for new ('SparseImagingExperiment'-based) classes
• Cleaned up unit tests for statistical methods

Cardinal 2.1.8

BUG FIXES

• Updated 'PositionDataFrame' initialization due to change in S4Vectors [<-,DataFrame behavior
• Updated 'MassDataFrame' initialization due to change in S4Vectors [<-,DataFrame behavior

Cardinal 2.1.7

BUG FIXES

• Updated 'filter' signature due to dplyr changes

Cardinal 2.1.6

SIGNIFICANT USER-VISIBLE CHANGES

• Added ImmunoOncology biocViews term

Cardinal 2.1.5 (2018-12-14)

BUG FIXES

• Updated read/write methods for 'matter' filemode changes

Cardinal 2.1.4 (2018-12-12)

SIGNIFICANT USER-VISIBLE CHANGES

• In 'readImzML' and 'readAnalyze', changed defaults from 'attach.only=FALSE' to 'attach.only=TRUE'
• In 'readImzML' and 'readAnalyze', changed defaults from 'as=MSImageSet' to 'as=MSImagingExperiment'

BUG FIXES

• Subsetting large 'SparseImagingExperiment' objects with 'sparse_mat' imageData should no longer hang

Cardinal 2.1.3 (2018-12-12)

NEW FEATURES

• Added 'ImagingResult' class for results of statistical analyses of imaging experiments
• Added 'spatialFastmap' method for 'SparseImagingExperiment'
• Updated 'summarize' to accept a '.group_by' argument
• Added 'simulateSpectrum' and 'simulateImage' functions

SIGNIFICANT USER-VISIBLE CHANGES

• Automatically detect and setup 'layout' for new classes
• Using 'layout' now assumes (row, column) order when creating facet plots for new classes (only)
• Updated examples in documentation to use new classes

BUG FIXES

• Fixed bug in 'spatialKMeans' that caused 'spatialFastmap' to fail for datasets with fewer features than components
• Fixed bug where 'plot' did not facet over runs of a 'SparseImagingExperiment' when using 'plusminus'

Cardinal 2.1.2 (2018-11-30)

SIGNIFICANT USER-VISIBLE CHANGES

• Updated 'spatialKMeans' to use new 'spatialFastmap'
• Updated 'spatialShrunkenCentroids' to use new spatially-aware discriminant scores calculation

Cardinal 2.1.1 (2018-11-30)

NEW FEATURES

• Added 'spatialFastmap' method for performing spatially-aware FastMap projection more easily

Cardinal 2.0.2 (2018-11-30)

BUG FIXES

• Fixed bug in 'reduceDimension.peaks' that caused peak intensities to be binned incorrectly

Cardinal 2.0.1 (2018-11-14)

SIGNIFICANT USER-VISIBLE CHANGES

• Updated 'peakFilter' to check for freq.min >= 1 to accomodate old behavior (counts)

Cardinal 1.99.2 (2018-10-28)

SIGNIFICANT USER-VISIBLE CHANGES

• Updated vignettes for Cardinal 2.0

BUG FIXES

• Removed a unit test broken on Windows

Cardinal 1.99.1 (2018-10-26)

NEW FEATURES

• Added vignettes and documentation for Cardinal 2.0

Cardinal 1.99.0 (2018-10-25)

SIGNIFICANT USER-VISIBLE CHANGES

• Version bump for Cardinal v2 release candidate

Cardinal 1.13.3 (2018-10-24)

NEW FEATURES

• Added 'process' method for queueing delayed processing functions to an imaging dataset and applying them
• Added new processing methods for Cardinal v2 including new versions of 'normalize', 'smoothSignal', 'reduceBaseline', 'peakPick', 'peakAlign', and 'peakFilter'
• Added new 'peakBin' function for binning peaks
• Updated 'show' method for new Cardinal v2 classes
• New support for exporting 'processed' imzML files via the 'writeImzML' function

Cardinal 1.13.2

NEW FEATURES

• Added new classes for Cardinal v2 including 'XDataFrame', 'PositionDataFrame', 'MassDataFrame', 'ImagingExperiment', 'SparseImagingExperiment', and 'MSImagingExperiment'

Cardinal 1.13.1

SIGNIFICANT USER-VISIBLE CHANGES

• Updated installation instructions for "CardinalWorkflows"

Cardinal 1.12.1

BUG FIXES

• Fixed bug in reading Analyze 7.5 files

Cardinal 1.11.2

NEW FEATURES

• Added 'writeMSIData', 'writeImzML', and 'writeAnalyze' methods for writing MSI data to supported file formats
• Added support for on-disk 'processed' imzML (via argument 'attach.only' in 'readImzML' method)

SIGNIFICANT USER-VISIBLE CHANGES

• Package 'matter' is used for all file I/O now
• Switched from using 'Hashmat' to using 'sparse_mat' class from 'matter' for 'processed' imzML data

BUG FIXES

• Changed compiler settings for parsing XML so reading large imzML files should use much less memory now (but may take slightly longer for smaller files)

Cardinal 1.11.1 (2017-10-25)

SIGNIFICANT USER-VISIBLE CHANGES

• Use 'drop=NULL' from now on instead of 'drop=NA' to do endomorphic subsetting of 'SimageData' objects

BUG FIXES

• Use 'keys' and 'keys<-' generic from 'matter'

Cardinal 1.9.2 (2017-10-25)

BUG FIXES

• Corrected author name in all documentation

Cardinal 1.9.1 (2017-10-23)

BUG FIXES

• Fixed bug in package dependency 'matter' affecting the size of datasets that can be processed with 'batchProcess'
• Fixed bug where bin sizes for units='ppm' were twice as wide as they should be in 'readImzML' and 'reduceDimension'

Cardinal 1.7.2

SIGNIFICANT USER-VISIBLE CHANGES

• In 'image' method, 'superpose = TRUE' now supports multiple LHS arguments in the formula (e.g., formula = a + b ~ x * y)

Cardinal 1.7.1 (2016-11-29)

NEW FEATURES

• PCA is now supported for larger-than-memory on-disk datasets
• External 'matter' matrices replace 'Binmat' matrices for on-disk support
• Added 'image3D' aliases for all 'ResultSet' subclasses

SIGNIFICANT USER-VISIBLE CHANGES

• Added 'matter' package to Depends list

Cardinal 1.5.2

SIGNIFICANT USER-VISIBLE CHANGES

• Updated 'batchProcess' to support reduceDimension and peakAlign
• Now 'peakAlign' looks for an existing 'mean' column in featureData
• Added 'matter' support to readAnalyze (previously only readImzML)

BUG FIXES

• Fixed bug when indexing into data cube using 'imageData' method

Cardinal 1.5.1

BUG FIXES

• Corrected author and maintainer contact information

Cardinal 1.5.0

NEW FEATURES

• Added experimental support for 'matter' on-disk matrices, from package 'matter', hosted at https://github.com/kuwisdelu/matter, as a replacement for 'Binmat' matrices

BUG FIXES

• Fixed subsetting SImageData objects with variables

Cardinal 1.3.3

BUG FIXES

• Subsetting the S4 part of Binmat objects by row is now an error
• Providing non-positive m/z values to 'readImzML' is now an error
• Elements of 'imageData' that fail to 'combine' or which are missing from one or more of the objects are now dropped from the result with warning rather than failing
• Moved unit tests in 'ints/tests' to 'tests/testthat'

Cardinal 1.3.2

NEW FEATURES

• Added 'image3D' method for plotting 3D images
• Added 'batchProcess' method for batch pre-processing

Cardinal 1.3.1

SIGNIFICANT USER-VISIBLE CHANGES

• Added 'mass.accuracy' and 'units.accuracy' arguments for controlling the m/z accuracy when reading 'processed' imzML
• Function 'reduceDimension.bin' now takes argument 'units' with value 'ppm' or 'mz', and new corresponding defaults

BUG FIXES

• Fixed bug in reading 'processed' imzML format that caused mass spectra to be reconstructed in the wrong order
• Improved speed accessing columns of Hashmat sparse matrices
• In 'pixelApply' and 'featureApply', zero-length return values are no longer returned as a list when '.simplify=FALSE'
• Function 'peakAlign.diff' should be more memory efficient now

Cardinal 1.3.0 (2015-12-16)

NEW FEATURES

• Added experimental Binmat class for working with on-disk matrices
• Added experimental support for 3D files from benchmark datasets
• Added experimental support for plotting 3D images
• Added experimental support for 'processed' imzML format

SIGNIFICANT USER-VISIBLE CHANGES

• Added 'attach.only' argument to readImzML and readAnalyze

BUG FIXES

• Fixed bug in plotting 3D image slices in the z dimension
• Fixed bug where large imzML files could not be read due to byte offsets being stored as ints; they are now stored as doubles.
• Fixed bug with strip labels in 3D plotting and with mixed labels
• Fixed bug with unique m/z feature names for high mass resolutions

Cardinal 1.1.0

BUG FIXES

• Fixed bug in formatting m/z labels affecting R 3.2.2
• Removed dependency on 'fields' because 'maps' is broken on Windows

Cardinal 0.99.6

SIGNIFICANT USER-VISIBLE CHANGES

• Bioconductor Release Candidate 7
• Added CITATION file for citing Cardinal

BUG FIXES

• In 'readAnalyze' and 'readMSIData', removed endianness check in Analyze 7.5 headers because some ABSciex data files specify an incorrect header size, thereby fixing a bug where bits would be swapped wrongly and file read incorrectly.

Cardinal 0.99.5

SIGNIFICANT USER-VISIBLE CHANGES

• Bioconductor Release Candidate 6
• Added new vignette for Cardinal design and development
• Now using ProtGenerics generics for 'spectra', 'peaks', and 'mz'

Cardinal 0.99.4

SIGNIFICANT USER-VISIBLE CHANGES

• Bioconductor Release Candidate 5
• Updated vignette with biological examples
• Added new citations to vignette

Cardinal 0.99.3

SIGNIFICANT USER-VISIBLE CHANGES

• Bioconductor Release Candidate 4
• In plot and image methods, 'groups' arg now coerced to factor

BUG FIXES

• Fixed bug in subset arg in select method
• Fixed bug in plot and image methods with NA in 'groups' arg

Cardinal 0.99.2

SIGNIFICANT USER-VISIBLE CHANGES

• Bioconductor Release Candidate 3
• Adjusts NIPALS unit tests for Windows build

Cardinal 0.99.1

SIGNIFICANT USER-VISIBLE CHANGES

• Bioconductor Release Candidate 2
• Cleaned up biocViews

BUG FIXES

• Fixed bug in SImageData coord factor levels not being properly updated when SImageSet is subsetted

Cardinal 0.99.0 (2014-12-22)

SIGNIFICANT USER-VISIBLE CHANGES

• Bioconductor Release Candidate 1

Cardinal 0.9.0 (2014-12-22)

SIGNIFICANT USER-VISIBLE CHANGES

• Added standardizeSamples method for between-sample normalization

Cardinal 0.8.9

SIGNIFICANT USER-VISIBLE CHANGES

• Improved plot methods for object summaries
• Fixed minor issurs in walkthrough vignette

Cardinal 0.8.8 (2014-11-27)

SIGNIFICANT USER-VISIBLE CHANGES

• Changed modelData for ResultSet from facors to original parameters
• Added plot method for summaries of ResultSet objects
• Added 'normalize.image' argument for image method
• Improved plot and image methods for CrossValidated

Cardinal 0.8.7 (2014-11-23)

SIGNIFICANT USER-VISIBLE CHANGES

• Completed Cardinal-walkthrough vignette

BUG FIXES

• Fixed bug in plotting vectors from ResultSet
• Fixed bug in PCA summary in reporting explained variance

Cardinal 0.8.6 (2014-11-21)

SIGNIFICANT USER-VISIBLE CHANGES

• Completed walkthrough vignettes
• Added ImagingMassSpectrometry biocView

Cardinal 0.8.5 (2014-11-20)

SIGNIFICANT USER-VISIBLE CHANGES

• Added 'show' and 'print' methods for most objects
• Changed 'combine' method for IAnnotatedDataFame, SImageData, and SImageSet
• Completed .Rd documentation for all public methods
• Cleaned up R CMD check warnings (except C++ .hpp headers)

BUG FIXES

• Fixed bug in between-cluster SS calculation for spatialKMeans
• Fixed bug with pre-processing 1-pixel datasets

Cardinal 0.8.4 (2014-10-16)

SIGNIFICANT USER-VISIBLE CHANGES

• Changed 'topIons' to 'topLabels' method for summarization
• Added MSImageData class for peakData and mzData methods
• Changed naming scheme for SImageData (.iData => iData)

BUG FIXES

• Fixed bug in plotting of classes for SpatialShrunkenCentroids
• Fixed bug in fopen in readAnalyze and readImzML affecting Windows

Cardinal 0.8.3

SIGNIFICANT USER-VISIBLE CHANGES

• Added 'coregistration' for SpatialKMeans
• Added 'summary' methods for all ResultSet subclasses
• Added 'topIons' method for summarization
• Added plotting methods for 'ResultSet' classes
• Added 'cvApply' method for cross-validation
• Added additional statistics to SpatialKmeans class results
• Changed 'auto.key' argument to 'key' in plotting methods

BUG FIXES

• Fixed bug in spatialShrunkenCentroids with prior probabilties
• Fixed bug in OPLS with proper scaling of data matrices during prediction

Cardinal 0.8.2

SIGNIFICANT USER-VISIBLE CHANGES

• Added 'peakFilter' method
• Minor fixes to documentation

Cardinal 0.8.1

SIGNIFICANT USER-VISIBLE CHANGES

• Changed 'parameters' argument to 'model' for ResultSet plot and image
• Added 'auto.key' to plot and image for when 'groups' are specified
• Added strip labels to plot and image when using base graphics
• Added 'coregister' method for 'SpatialShrunkenCentroids'
• Method 'image' is now vectorized for argument 'mz'
• Method 'plot' is now vectorized for argument 'coord'

BUG FIXES

• Fixed a bug where conditions are plotted in an incorrect order

Cardinal 0.8.0

SIGNIFICANT USER-VISIBLE CHANGES

• First public beta available for ASMS 2014.

Cardinal 0.7

SIGNIFICANT USER-VISIBLE CHANGES

• Refactored version of the package prepared for internal testing.
• New processing methods, renamed to 'normalize', 'smoothSignal', 'reduceBaseline', 'peakPick', 'peakAlign', 'reduceDimension'.
• New function 'readMSIData' for reading supported formats.
• Native support for imzML added (no longer requires Java).
• Methods 'pixels' and 'features' replaced with updated versions.
• In 'features' method, m/z matching now done using bisection search.
• New analysis method, renamed to spatialShrunkenCentroids.
• Analysis methods now return a new class: 'ResultSet'.
• New method 'select' to replace 'selectROI' and 'selectPixels'.

Cardinal 0.6

SIGNIFICANT USER-VISIBLE CHANGES

• Major revision to use Bioconductor base packages.
• New dependencies on BiocGenerics and Biobase.
• New virtual class iSet for generic imaging data.
• New classes ImageSet, SImageSet, ImageData, and SImageData.
• Revised MSImageSet that uses new parent classes.
• New class MIAPE-Imaging for Minimum Information About a Protemics Experiment - Imaging.
• New class MSImageProcess for pre-processing information.
• Revised functions for importing Analyze 7.5 and imzML
• New plotting and image methods using lattice-style formula interface.
• New pixelApply and featureApply methods.

Cardinal 0.5

SIGNIFICANT USER-VISIBLE CHANGES

• Added image coregistration for 3D sections.
• Added 'volume' method for 3D visualization.

Cardinal 0.4

SIGNIFICANT USER-VISIBLE CHANGES

• Added 'summaryPlot' method for segmentation visualization.
• Exposed 'calibrateSegmentation' method to calibrate colors between multiple MSImageSegmentation objects.
• Added more thorough verbose output for 'spatialSparseCluster' and 'spatialSparseKMeans' methods.
• Improved behavior of 'intensities' method when reconstructing complex datacubes and with non-contiguous pixel requests.
• Changed 'trellisImage' to plot all coordinates for dimensions omitted from 'fixCoord' by default.
• Minor changes to the 'MSImageSegmentation' class structure.
• Improved 'likPlot' method and added AIC and BIC results and the resulting number of classes.

Cardinal 0.3

SIGNIFICANT USER-VISIBLE CHANGES

• Improved speed of imaging processing (smoothing and interpolation) methods for use with 'image' and 'trellisImage'.
• Added option for verbose output and hooks for GUI progress bars.
• For prediction on 'MSImageSegmentation' objects, 'autoDimNames' is now automatically passed along from the original call.
• Changed 'MSImageSegmentation' to an S4 class derived from 'list'.
• Added option for plotting the probabilities of an 'MSImageSegmentation' using overlaid transparency masks for improved visualization.

Cardinal 0.2

SIGNIFICANT USER-VISIBLE CHANGES

• Package renamed from internal code-name "Canary" to "Cardinal".
• Split off GUI to a new package called "CardinaliView".
• New GUI in "CardinaliView" now based on gWidgets and RGtk2.
• Added slot 'peaks' to 'MSImageSet' class.
• Changed 'MSPeakFrame' and 'MSPeakList' to S4 classes, and added new class 'MSPeak Alignment'.
• Changed how the 'estimateNoise' method estimates noise.
• Changed options in the 'detectPeaks' method to be more useful.
• Changed the 'alignPeaks' methods to align to the mean spectrum as a reference when aligning a list of peaks.
• Added 'interpolate' option for images.
• Added new method "selectPeaks" for manual peak selection.
• Modified the 'type' arguments in the plotting methods.
• Changed 'crossValidate' method to now return predictions for the full dataset for every fold instead of the test set only.

BUG FIXES

• Fixed bug where plotting mass spectra for multiple pixels fails on datasets with missing mass spectra.
• Fixed bug where the 'unload' method did not remove the object.
• Fixed bug in the 'crossValidate' method where the dots arguments were not passed to the 'predict' method.

Cardinal 0.1

SIGNIFICANT USER-VISIBLE CHANGES

• First internal release for Stanford Canary Center for Cancer Early Detection as primary beta testers.
• Implementation of MSImageSet S4 class; mass spectra are stored as a flat matrix with rows as features and columns as pixels; original data cube can be reconstructed dynamically using a position array; spectra stored using environments to prevent redundant data copying.
• Visualization that includes plotting ion images and mass spectra, using both base graphics and lattice graphics, allowing trellis display of multiple ion images and multipe mass spectra.
• Pre-processing for that includes normalization, baseline correct, peak-picking, peak-alignment, resampling, and binning.
• Multivaritate statistical analysis includes PCA, PLS, and OPLS.
• Supervised analysis includes a spatially-aware version of nearest shrunken centroids, PLS-DA, and OPLS-DA.
• Unsupervised analysis includes spatially-aware clustering based on nearest shrunken centroids, and an implementation based on sparse k-means.
• GUI based on tcltk using rpanel that supports all major processing and statistical analysis methods in the package, except for PLS and OPLS.