CHANGES IN VERSION 3.2.1 [2023-5-2] ----------------------------------- BUG FIXES o Cleaned up escaped LaTeX specials in documentation o Fixed 'sprintf()' => 'snprintf()' warning in C code CHANGES IN VERSION 3.0.1 [2022-11-14] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Overwriting existing MSI files is now a warning instead of an error BUG FIXES o Fixed issue in 'peakAlign()' reference m/z's being sort and unique CHANGES IN VERSION 2.99.1 [2022-10-31] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Updated vignettes for Cardinal 3 o Widened default m/z 'tolerance' for sparse spectra o Switched to linear interpolation for sparse spectra CHANGES IN VERSION 2.99.0 [2022-10-26] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Updated out-of-memory backend to Matter 2.0 o Removed support for legacy classes and methods CHANGES IN VERSION 2.11.3 [2021-9-15] ----------------------------------- BUG FIXES o Fix strange behavior from random number generation in R >= 4.1.1 CHANGES IN VERSION 2.11.2 [2021-8-5] ----------------------------------- BUG FIXES o Fix reference naming scheme for binning and alignment methods CHANGES IN VERSION 2.11.1 [2021-7-26] ----------------------------------- BUG FIXES o Use as(x, 'DFrame') instead of as(x, 'DataFrame') o Fix logical length > 1 error in 'segmentationTest()' CHANGES IN VERSION 2.7.2 [2020-10-21] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o For 'mzAlign()', the 'ref' parameter now expects a vector of reference m/z-values rather than a complete spectrum CHANGES IN VERSION 2.7.1 [2020-6-30] ----------------------------------- BUG FIXES o Fixed issue where 'spatialDGMM()' would sometimes fail for features with singular segmentations o Suppressed warnings on 'Mclust()' initialization to 'spatialDGMM()' caused by R 4.0 changes o Fixed pixel/feature mapping in 'spatialDGMM()' metadata CHANGES IN VERSION 2.5.12 [2020-4-24] ----------------------------------- BUG FIXES o Drawing a region-of-interest using 'selectROI()' should now update the plot properly in RStudio devices o Fixed issues with automatically guessing a reasonable mass tolerance for certain pre-processing methods o In 'mzBin()', the previous value of 'centroided()' from the original dataset is now preserved after binning CHANGES IN VERSION 2.5.11 [2020-4-23] ----------------------------------- BUG FIXES o Fixed bug in 'spatialShrunkenCentroids()' that produced in NaNs when discriminant scores were very large o Fixed bug in 'spatialFastmap()' where subsetting produced vectors instead of matrices due to omitting 'drop=FALSE' CHANGES IN VERSION 2.5.10 [2020-4-22] ----------------------------------- NEW FEATURES o Added 'topFeatures()' method for 'spatialKMeans()' o Added coercion to 'DataFrame' from 'MSImagingExperiment' SIGNIFICANT USER-VISIBLE CHANGES o 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 CHANGES IN VERSION 2.5.9 [2020-4-22] ----------------------------------- NEW FEATURES o Added 'aggregate()' method for imaging experiments including 'summarizePixels()' and 'summarizeFeatures()' o Added 'subset()' method for imaging experiments including 'subsetPixels()' and 'subsetFeatures()' SIGNIFICANT USER-VISIBLE CHANGES o 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 o Fix bug in 'spatialDGMM()' printing caused by a change in default.stringsAsFactors() == FALSE in R 4.0 CHANGES IN VERSION 2.5.8 [2020-4-18] ----------------------------------- NEW FEATURES o Automatic estimation of mass resolution will now work for 'processed' imzML with centroid spectra o New getter/setter options for Cardinal options such as 'getCardinalBPPARAM()' and 'setCardinalBPPARAM()' SIGNIFICANT USER-VISIBLE CHANGES o Default BPPARAM backend is now set to 'SerialParam()'; use 'setCardinalBPPARAM()' to change the backend o Expose '.view' argument of 'matter::chunk_apply()' in 'pixelApply()', 'featureApply()', and 'spatialApply()' o Previously-deprecated functions 'generateSpectrum()' and 'generateImage()' are now defunct o Removed defunct functions 'Binmat()' and 'topLabels()' BUG FIXES o Fix large intensity text cutoffs in 'image()' colorkey CHANGES IN VERSION 2.5.7 [2020-3-30] ----------------------------------- BUG FIXES o Fix bug when using 'rbind()' or 'cbind()' on 'MassDataFrame' and 'PositionDataFrame' CHANGES IN VERSION 2.5.6 [2020-3-24] ----------------------------------- BUG FIXES o Fix bug when assigning a dense matrix via iData()<- for an 'MSProcessedImagingExperiment' object CHANGES IN VERSION 2.5.5 [2020-3-14] ----------------------------------- BUG FIXES o Fix bug in 'show' method for 'SimpleImageList' caused by class(matrix) -> c("matrix", "array") CHANGES IN VERSION 2.5.4 [2020-3-13] ----------------------------------- BUG FIXES o Fix bugs in legacy classes caused by a change in default.stringsAsFactors() == FALSE in R 4.0 CHANGES IN VERSION 2.5.3 [2020-3-13] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o The 'resolution' argument in all methods has been redefined to always mean **full bin widt for both "mz" and "ppm" units CHANGES IN VERSION 2.5.2 [2020-3-2] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o The 'pixelApply()', 'featureApply()', and 'spatialApply()' methods now internally use 'matter::chunk_apply()' CHANGES IN VERSION 2.5.1 [2020-1-22] ----------------------------------- BUG FIXES o Fixed bug in 'mzBin()' binning spectra incorrectly o Fixed bug in contrast enhancement with missing intensities CHANGES IN VERSION 2.3.18 [2019-10-27] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Processing in 'crossValidate()' now allows processing unprocessed data by performing peak-picking on the mean spectra of the training sets BUG FIXES o Fixed some errors in user messages during peak processing CHANGES IN VERSION 2.3.17 [2019-10-25] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Default for 'peakBin()' argument 'type' is now "area" o In 'peakBin()', peak boundaries should be calculated more accurately now, and general speed improvements o In 'peakAlign()', peak centers are now calculated as weighted average mass rather than the highest point CHANGES IN VERSION 2.3.16 [2019-10-14] ----------------------------------- NEW FEATURES o New class 'ImagingSummary' with sub-classes including 'SparseImagingSummary' and 'MSImagingSummary' with appropriate 'plot()' and 'image()' methods SIGNIFICANT USER-VISIBLE CHANGES o 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"' CHANGES IN VERSION 2.3.15 [2019-10-13] ----------------------------------- NEW FEATURES o For methods requiring 'resolution' or 'tolerance', the default arguments have been updated to automatically guess based on the data CHANGES IN VERSION 2.3.14 [2019-5-26] ----------------------------------- NEW FEATURES o Add spectraData() as an alias for 'imageData()' for 'MSImagingExperiment' sub-classes o Formalize 'mzData()' and 'intensityData()' getters and setters for 'MSProcessedImagingExperiment' o Add 'peaks()' and 'peakData()' methods for extracting peak matrices and/or peak information o Add 'isCentroided()' method for guessing whether spectra are centroided (without using the @centroided slot) SIGNIFICANT USER-VISIBLE CHANGES o Allow 'NA' for @centroided slot for 'MSImagingExperiment' o 'mzBin()' method now sets centroided = NA o Update 'mzFilter()' with parameter defaults so that 'thresh.max = NA' and new arg 'rm.zero = TRUE' o Log more pre-processing information (e.g., method name) CHANGES IN VERSION 2.3.13 [2019-5-23] ----------------------------------- BUG FIXES o Try using 'parent.frame(1)' instead of 'parent.frame(2)' to fix NSE methods when used in LHS of a maggritr pipe o Fix weird 'iData()<-' missing argument 'i' bug CHANGES IN VERSION 2.3.12 [2019-5-22] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Changed default 'peakPick()' method to 'mad' o In 'peakPick()' method 'mad', change the default number of blocks to 1 (no adaptive smoothing) o In 'peakPick()' method 'mad', update w/ new arguments w/ new defaults 'fun=median' and 'tform=diff' BUG FIXES o In 'peakPick()' methods 'simple' and 'adaptive', warn if kurtosis cannot be estimated and try to recover o In 'normalize()' method 'reference', provide a warning if the reference value is 0 for a pixel CHANGES IN VERSION 2.3.11 [2019-5-19] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Improved speed in 'spatialFastmap()' o Improved speed in 'spatialShrunkenCentroids()' o New dissimilarity metrics for 'spatialFastmap()' including a new default metric='average' BUG FIXES o Fix error in 'print()' for facet plots where lims=NULL CHANGES IN VERSION 2.3.10 [2019-5-18] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Improved speed in 'spatialDGMM()', by moving spatial filtering of probabilities to C code, up to 10x faster o Linesearch in 'spatialDGMM()' now uses 'optimize()' rather than 'optim()' -- results may differ slightly CHANGES IN VERSION 2.3.9 [2019-5-17] ----------------------------------- NEW FEATURES o Added 'Cardinal.history()' and 'Cardinal.version()' SIGNIFICANT USER-VISIBLE CHANGES o Removed under-used setter generic function definitions BUG FIXES o Cleaned up generics to reflect ProtGenerics >= 1.17.2 CHANGES IN VERSION 2.3.8 [2019-5-16] ----------------------------------- NEW FEATURES o Added boxplot, histogram, and bar chart functionality to the 'plot()' method for 'XDataFrame' o Added 'plot()' plotting for 'AnnotatedImageList' o Added 'plot()' methods for 'SpatialDGMM', 'MeansTest', and 'SegmentationTest' result classes o Added 'image()' method for 'MeansTest' result class SIGNIFICANT USER-VISIBLE CHANGES o Updated 'plot()' and 'image()' methods for 'SpatialDGMM', 'MeansTest', and 'SegmentationTest' result classes BUG FIXES o Various bug fixes in object printing and plot auto-layout CHANGES IN VERSION 2.3.7 [2019-5-13] ----------------------------------- NEW FEATURES o Added 'image()' plotting for 'AnnotatedImageList' BUG FIXES o Plotting with 'add=TRUE' now respects 'par('usr')' coordinates CHANGES IN VERSION 2.3.6 [2019-5-13] ----------------------------------- NEW FEATURES o Add 'AnnotatedImageList' class for list of 'AnnotatedImage' objects o Add 'AnnotatedImagingExperiment' class for containing data for an optical imaging experiment (e.g., a microscopy experiments) o Add 'image()' plotting for 'AnnotatedImagingExperiment' SIGNIFICANT USER-VISIBLE CHANGES o Redefine '@featureData' slot of a 'SparseImagingExperiment' to be a 'DataFrame' rather than requiring an 'XDataFrame' BUG FIXES o Respect 'layout' and 'byrow' passed through ... args to 'print()' method on facet plot objects CHANGES IN VERSION 2.3.5 [2019-5-11] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o 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 o Pass more ... args through to 'par()' in plotting functions CHANGES IN VERSION 2.3.4 [2019-5-10] ----------------------------------- NEW FEATURES o Added 'AnnotatedImage' class for optical images CHANGES IN VERSION 2.3.3 [2019-5-10] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Improved facet plotting when 'add=TRUE' BUG FIXES o Better 'cex.axis' defaults and user setting for colorkeys CHANGES IN VERSION 2.3.2 [2019-5-9] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Improved 'writeMSIData()' for 3D and non-gridded data CHANGES IN VERSION 2.3.1 [2019-5-8] ----------------------------------- NEW FEATURES o Output directly to imzML while processing with 'process()' SIGNIFICANT USER-VISIBLE CHANGES o Improved auto-layout for visualization with multiple runs o Added 'parse.only' option to 'readImzML()' for parsing only CHANGES IN VERSION 2.2.4 [2019-5-8] ----------------------------------- BUG FIXES o Fix large external array offsets in 'writeImzML' CHANGES IN VERSION 2.2.3 [2019-5-8] ----------------------------------- BUG FIXES o Cleaned up some 'writeImzML' mapping validity issues CHANGES IN VERSION 2.2.2 [2019-5-7] ----------------------------------- BUG FIXES o Removed curly braces around UUID when writing imzML CHANGES IN VERSION 2.2.1 [2019-5-6] ----------------------------------- BUG FIXES o Fixed bug in plotting results where 'column' argument would get matched before the 'col' argument CHANGES IN VERSION 2.1.30 [2019-4-30] ----------------------------------- BUG FIXES o Fixed bug where 'spatialShrunkenCentroids' classification would change the user 'options(Cardinal.progress)' CHANGES IN VERSION 2.1.29 [2019-4-29] ----------------------------------- BUG FIXES o Coercing to 'SpatialShrunkenCentroids2' now drops empty classes for segmentations (as expected) CHANGES IN VERSION 2.1.28 [2019-4-28] ----------------------------------- BUG FIXES o Fixed 'topFeatures' method for 'SpatialShrunkenCentroids2' where 'statistic' was actually printing the 'centers' o The 'collect' method for 'MSProcessedImagingExperiment' now preserves sparseness when pulling into memory CHANGES IN VERSION 2.1.27 [2019-4-26] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Added 'mzFilter' as an alias for 'peakFilter' with more suitable defaults for non-peak-picked spectra BUG FIXES o Minor fixes to 'print' method for plots and images o Minor fixes to margin padding for 'colorkey' in images CHANGES IN VERSION 2.1.26 [2019-4-25] ----------------------------------- BUG FIXES o Fixed 'print' method for plots and images to respect updating plotting parameters via '...' arguments CHANGES IN VERSION 2.1.25 [2019-4-25] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Add 'run' argument to 'pixels' for 'MSImagingExperiment' o Add 'run' argument to 'plot' for 'MSImagingExperiment' BUG FIXES o Fixed bug in 'ylab' with one-sided formulas in 'plot' o Relaxed errors for out-of-range m/z values in 'features' o Value range of 'colorkey' now obeys 'zlim' argument o NULL values for plot limits no longer give errors CHANGES IN VERSION 2.1.24 [2019-4-24] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Documented new 'options(Cardinal.dark=FALSE)' default BUG FIXES o Fixed linear subsetting of models using '['' for 'SparseImagingResult' objects o Check length of 'classControl' in 'segmentationTest' CHANGES IN VERSION 2.1.23 [2019-4-24] ----------------------------------- NEW FEATURES o Added 'slice' for slicing imaging datasets (as a data cube) o Added 'alpha.power' argument for 'image' methods SIGNIFICANT USER-VISIBLE CHANGES o Added documentation for options() under '?Cardinal' CHANGES IN VERSION 2.1.22 [2019-4-24] ----------------------------------- NEW FEATURES o Added new 'Cardinal 2: Statistical methods' vignette CHANGES IN VERSION 2.1.21 [2019-4-23] ----------------------------------- NEW FEATURES o Added 'image3D' methods for new classes CHANGES IN VERSION 2.1.20 [2019-4-23] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Updated documentation and simulation examples BUG FIXES o Fixed bug in 'summary' for 'SpatialShrunkenCentroids2' CHANGES IN VERSION 2.1.19 [2019-4-23] ----------------------------------- NEW FEATURES o Added 'colocalized' method for colocalization CHANGES IN VERSION 2.1.19 [2019-4-23] ----------------------------------- NEW FEATURES o Added 'colocalized' method for colocalization CHANGES IN VERSION 2.1.18 [2019-4-23] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Updated 'Cardinal 2: User guide' vignette BUG FIXES o Fixed bug in 'simulateSpectrum' when n > 1 CHANGES IN VERSION 2.1.17 [2019-4-22] ----------------------------------- NEW FEATURES o Added 'topFeatures' method for extracting top-ranked features from statistical analyses o Added 'summary' methods for new results objects o Added 'SummaryDataFrame' for printing result summaries SIGNIFICANT USER-VISIBLE CHANGES o Deprecated 'topLabels' method -> use 'topFeatures' CHANGES IN VERSION 2.1.16 [2019-4-20] ----------------------------------- NEW FEATURES o Added dplyr verbs for 'DataFrame' and "XDataFrame' CHANGES IN VERSION 2.1.15 [2019-4-19] ----------------------------------- NEW FEATURES o Added new 'PCA' method for 'SparseImagingExperiment' o Added new 'PLS' method for 'SparseImagingExperiment' o Added new 'OPLS' method for 'SparseImagingExperiment' SIGNIFICANT USER-VISIBLE CHANGES o The 'selectROI' method will now use the last plot if no additional plotting arguments are given o Setting 'resolution' on 'MSProcessedImagingExperiment' will now update the m/z values binning scheme o The 'select' and 'filter' methods now using integers as row/col IDs without the '.id' argument BUG FIXES o Fixed bug in 'OPLS' methods causing cross-validation to produce slightly optimistic results CHANGES IN VERSION 2.1.14 [2019-4-18] ----------------------------------- NEW FEATURES o New 'mzAlign' processing method for spectral alignment o New 'mzBin' processing method for spectral binning o New 'crossValidate' method that cleans up 'cvApply' output o New normalization methods: 'rms' and 'reference' o New baseline reduction method: 'locmin' o New peak picking method: 'mad' o New 'darkmode' and 'lightmode' plotting options o Added 'cvApply' methods for new classes SIGNIFICANT USER-VISIBLE CHANGES o Image plotting now uses different 'colorkey' legend placed beside plot that no longer obscures the image o All plotting now uses different 'strip' labels placed above plot that no longer obscures the plot area o All plotting now accept hidden 'dark=TRUE' argument to switch to plotting in new "dark mode" o Changed/updated presets for 'presetImageDef' which provides presets for 'simulateImage' function CHANGES IN VERSION 2.1.13 [2019-4-15] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Added message when printing a 'SparseImagingExperiment' object without un-applied pre-processing steps BUG FIXES o Added C routine registration with "C_" prefix for .Call o Cleaned up '.o' objects in /src created by accident CHANGES IN VERSION 2.1.12 [2019-4-14] ----------------------------------- NEW FEATURES o Added 'meansTest' method for linear model-based hypothesis tests of mean-summarized images o Added 'segmentationTest' method for linear model-based hypothesis tests of spatially-segmented images CHANGES IN VERSION 2.1.11 [2019-4-12] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Added option to set the probability regularization parameter (p0) to 'spatialDGMM' method o Added option to initialize 'spatialDGMM' algorithm with either k-means or Gaussian mixture model CHANGES IN VERSION 2.1.10 [2019-4-12] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Changed default colorscale for images to 'viridis' o Updated 'simulateImage' presets to handle multiple runs CHANGES IN VERSION 2.1.9 [2019-4-11] ----------------------------------- NEW FEATURES o Added 'spatialDGMM' method for fitting feature-wise spatially-aware Dirichlet Gaussian mixture models o Added 'predict' method for 'SpatialShrunkenCentroids2' BUG FIXES o Fixed 'spatialShrunkenCentroids' classification methods for new ('SparseImagingExperiment'-based) classes o Cleaned up unit tests for statistical methods CHANGES IN VERSION 2.1.8 [2019-4-1] ----------------------------------- BUG FIXES o Updated 'PositionDataFrame' initialization due to change in S4Vectors [<-,DataFrame behavior o Updated 'MassDataFrame' initialization due to change in S4Vectors [<-,DataFrame behavior CHANGES IN VERSION 2.1.7 [2019-2-21] ----------------------------------- BUG FIXES o Updated 'filter' signature due to dplyr changes CHANGES IN VERSION 2.1.6 [2019-1-4] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Added ImmunoOncology biocViews term CHANGES IN VERSION 2.1.5 [2018-12-14] ----------------------------------- BUG FIXES o Updated read/write methods for 'matter' filemode changes CHANGES IN VERSION 2.1.4 [2018-12-12] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o In 'readImzML' and 'readAnalyze', changed defaults from 'attach.only=FALSE' to 'attach.only=TRUE' o In 'readImzML' and 'readAnalyze', changed defaults from 'as=MSImageSet' to 'as=MSImagingExperiment' BUG FIXES o Subsetting large 'SparseImagingExperiment' objects with 'sparse_mat' imageData should no longer hang CHANGES IN VERSION 2.1.3 [2018-12-12] ----------------------------------- NEW FEATURES o Added 'ImagingResult' class for results of statistical analyses of imaging experiments o Added 'spatialFastmap' method for 'SparseImagingExperiment' o Updated 'summarize' to accept a '.group_by' argument o Added 'simulateSpectrum' and 'simulateImage' functions SIGNIFICANT USER-VISIBLE CHANGES o Automatically detect and setup 'layout' for new classes o Using 'layout' now assumes (row, column) order when creating facet plots for new classes (only) o Updated examples in documentation to use new classes BUG FIXES o Fixed bug in 'spatialKMeans' that caused 'spatialFastmap' to fail for datasets with fewer features than components o Fixed bug where 'plot' did not facet over runs of a 'SparseImagingExperiment' when using 'plusminus' CHANGES IN VERSION 2.1.2 [2018-11-30] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Updated 'spatialKMeans' to use new 'spatialFastmap' o Updated 'spatialShrunkenCentroids' to use new spatially-aware discriminant scores calculation CHANGES IN VERSION 2.1.1 [2018-11-30] ----------------------------------- NEW FEATURES o Added 'spatialFastmap' method for performing spatially-aware FastMap projection more easily CHANGES IN VERSION 2.0.2 [2018-11-30] ----------------------------------- BUG FIXES o Fixed bug in 'reduceDimension.peaks' that caused peak intensities to be binned incorrectly CHANGES IN VERSION 2.0.1 [2018-11-14] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Updated 'peakFilter' to check for freq.min >= 1 to accomodate old behavior (counts) CHANGES IN VERSION 1.99.2 [2018-10-28] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Updated vignettes for Cardinal 2.0 BUG FIXES o Removed a unit test broken on Windows CHANGES IN VERSION 1.99.1 [2018-10-26] ----------------------------------- NEW FEATURES o Added vignettes and documentation for Cardinal 2.0 CHANGES IN VERSION 1.99.0 [2018-10-25] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Version bump for Cardinal v2 release candidate CHANGES IN VERSION 1.13.3 [2018-10-24] ----------------------------------- NEW FEATURES o Added 'process' method for queueing delayed processing functions to an imaging dataset and applying them o Added new processing methods for Cardinal v2 including new versions of 'normalize', 'smoothSignal', 'reduceBaseline', 'peakPick', 'peakAlign', and 'peakFilter' o Added new 'peakBin' function for binning peaks o Updated 'show' method for new Cardinal v2 classes o New support for exporting 'processed' imzML files via the 'writeImzML' function CHANGES IN VERSION 1.13.2 [2018-7-22] ----------------------------------- NEW FEATURES o Added new classes for Cardinal v2 including 'XDataFrame', 'PositionDataFrame', 'MassDataFrame', 'ImagingExperiment', 'SparseImagingExperiment', and 'MSImagingExperiment' CHANGES IN VERSION 1.13.1 [2018-7-22] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Updated installation instructions for "CardinalWorkflows" CHANGES IN VERSION 1.12.1 [2018-7-22] ----------------------------------- BUG FIXES o Fixed bug in reading Analyze 7.5 files CHANGES IN VERSION 1.11.2 [2017-12-2] ----------------------------------- NEW FEATURES o Added 'writeMSIData', 'writeImzML', and 'writeAnalyze' methods for writing MSI data to supported file formats o Added support for on-disk 'processed' imzML (via argument 'attach.only' in 'readImzML' method) SIGNIFICANT USER-VISIBLE CHANGES o Package 'matter' is used for all file I/O now o Switched from using 'Hashmat' to using 'sparse_mat' class from 'matter' for 'processed' imzML data BUG FIXES o 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) CHANGES IN VERSION 1.11.1 [2017-10-25] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Use 'drop=NULL' from now on instead of 'drop=NA' to do endomorphic subsetting of 'SimageData' objects BUG FIXES o Use 'keys' and 'keys<-' generic from 'matter' CHANGES IN VERSION 1.9.2 [2017-10-25] ----------------------------------- BUG FIXES o Corrected author name in all documentation CHANGES IN VERSION 1.9.1 [2017-10-23] ----------------------------------- BUG FIXES o Fixed bug in package dependency 'matter' affecting the size of datasets that can be processed with 'batchProcess' o Fixed bug where bin sizes for units='ppm' were twice as wide as they should be in 'readImzML' and 'reduceDimension' CHANGES IN VERSION 1.7.2 [2017-3-22] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o In 'image' method, 'superpose = TRUE' now supports multiple LHS arguments in the formula (e.g., formula = a + b ~ x * y) CHANGES IN VERSION 1.7.1 [2016-11-29] ----------------------------------- NEW FEATURES o PCA is now supported for larger-than-memory on-disk datasets o External 'matter' matrices replace 'Binmat' matrices for on-disk support o Added 'image3D' aliases for all 'ResultSet' subclasses SIGNIFICANT USER-VISIBLE CHANGES o Added 'matter' package to Depends list CHANGES IN VERSION 1.5.2 [2016-10-6] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Updated 'batchProcess' to support reduceDimension and peakAlign o Now 'peakAlign' looks for an existing 'mean' column in featureData o Added 'matter' support to readAnalyze (previously only readImzML) BUG FIXES o Fixed bug when indexing into data cube using 'imageData' method CHANGES IN VERSION 1.5.1 [2016-9-21] ----------------------------------- BUG FIXES o Corrected author and maintainer contact information CHANGES IN VERSION 1.5.0 [2016-5-25] ----------------------------------- NEW FEATURES o 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 o Fixed subsetting SImageData objects with variables CHANGES IN VERSION 1.3.3 [2016-4-20] ----------------------------------- BUG FIXES o Subsetting the S4 part of Binmat objects by row is now an error o Providing non-positive m/z values to 'readImzML' is now an error o 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 o Moved unit tests in 'ints/tests' to 'tests/testthat' CHANGES IN VERSION 1.3.2 [2016-3-29] ----------------------------------- NEW FEATURES o Added 'image3D' method for plotting 3D images o Added 'batchProcess' method for batch pre-processing CHANGES IN VERSION 1.3.1 [2016-3-14] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Added 'mass.accuracy' and 'units.accuracy' arguments for controlling the m/z accuracy when reading 'processed' imzML o Function 'reduceDimension.bin' now takes argument 'units' with value 'ppm' or 'mz', and new corresponding defaults BUG FIXES o Fixed bug in reading 'processed' imzML format that caused mass spectra to be reconstructed in the wrong order o Improved speed accessing columns of Hashmat sparse matrices o In 'pixelApply' and 'featureApply', zero-length return values are no longer returned as a list when '.simplify=FALSE' o Function 'peakAlign.diff' should be more memory efficient now CHANGES IN VERSION 1.3.0 [2015-12-16] ----------------------------------- NEW FEATURES o Added experimental Binmat class for working with on-disk matrices o Added experimental support for 3D files from benchmark datasets o Added experimental support for plotting 3D images o Added experimental support for 'processed' imzML format SIGNIFICANT USER-VISIBLE CHANGES o Added 'attach.only' argument to readImzML and readAnalyze BUG FIXES o Fixed bug in plotting 3D image slices in the z dimension o Fixed bug where large imzML files could not be read due to byte offsets being stored as ints; they are now stored as doubles. o Fixed bug with strip labels in 3D plotting and with mixed labels o Fixed bug with unique m/z feature names for high mass resolutions CHANGES IN VERSION 1.1.0 [2015-10-1] ----------------------------------- BUG FIXES o Fixed bug in formatting m/z labels affecting R 3.2.2 o Removed dependency on 'fields' because 'maps' is broken on Windows CHANGES IN VERSION 0.99.6 [2015-4-5] ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Bioconductor Release Candidate 7 o Added CITATION file for citing Cardinal BUG FIXES o 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. CHANGES IN VERSION 0.99.5 [2015-3-3] ------------------------------------ SIGNIFICANT USER-VISIBLE CHANGES o Bioconductor Release Candidate 6 o Added new vignette for Cardinal design and development o Now using ProtGenerics generics for 'spectra', 'peaks', and 'mz' CHANGES IN VERSION 0.99.4 [2015-2-15] ------------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Bioconductor Release Candidate 5 o Updated vignette with biological examples o Added new citations to vignette CHANGES IN Version 0.99.3 [2015-2-3] ------------------------------------ SIGNIFICANT USER-VISIBLE CHANGES o Bioconductor Release Candidate 4 o In plot and image methods, 'groups' arg now coerced to factor BUG FIXES o Fixed bug in subset arg in select method o Fixed bug in plot and image methods with NA in 'groups' arg CHANGES IN Version 0.99.2 [2015-1-20] ------------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Bioconductor Release Candidate 3 o Adjusts NIPALS unit tests for Windows build CHANGES IN Version 0.99.1 [2015-1-12] ------------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Bioconductor Release Candidate 2 o Cleaned up biocViews BUG FIXES o Fixed bug in SImageData coord factor levels not being properly updated when SImageSet is subsetted CHANGES IN Version 0.99.0 [2014-12-22] -------------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Bioconductor Release Candidate 1 CHANGES IN Version 0.9.0 [2014-12-22] ------------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Added standardizeSamples method for between-sample normalization CHANGES IN Version 0.8.9 [2014-12-5] ------------------------------------ SIGNIFICANT USER-VISIBLE CHANGES o Improved plot methods for object summaries o Fixed minor issurs in walkthrough vignette CHANGES IN Version 0.8.8 [2014-11-27] ------------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Changed modelData for ResultSet from facors to original parameters o Added plot method for summaries of ResultSet objects o Added 'normalize.image' argument for image method o Improved plot and image methods for CrossValidated CHANGES IN VERSION 0.8.7 [2014-11-23] ------------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Completed Cardinal-walkthrough vignette BUG FIXES o Fixed bug in plotting vectors from ResultSet o Fixed bug in PCA summary in reporting explained variance CHANGES IN Version 0.8.6 [2014-11-21] SIGNIFICANT USER-VISIBLE CHANGES o Completed walkthrough vignettes o Added ImagingMassSpectrometry biocView CHANGES IN Version 0.8.5 [2014-11-20] ------------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Added 'show' and 'print' methods for most objects o Changed 'combine' method for IAnnotatedDataFame, SImageData, and SImageSet o Completed .Rd documentation for all public methods o Cleaned up R CMD check warnings (except C++ .hpp headers) BUG FIXES o Fixed bug in between-cluster SS calculation for spatialKMeans o Fixed bug with pre-processing 1-pixel datasets CHANGES IN Version 0.8.4 [2014-10-16] ------------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Changed 'topIons' to 'topLabels' method for summarization o Added MSImageData class for peakData and mzData methods o Changed naming scheme for SImageData (.iData => iData) BUG FIXES o Fixed bug in plotting of classes for SpatialShrunkenCentroids o Fixed bug in fopen in readAnalyze and readImzML affecting Windows CHANGES IN Version 0.8.3 [2014-9-18] ------------------------------------ SIGNIFICANT USER-VISIBLE CHANGES o Added 'coregistration' for SpatialKMeans o Added 'summary' methods for all ResultSet subclasses o Added 'topIons' method for summarization o Added plotting methods for 'ResultSet' classes o Added 'cvApply' method for cross-validation o Added additional statistics to SpatialKmeans class results o Changed 'auto.key' argument to 'key' in plotting methods BUG FIXES o Fixed bug in spatialShrunkenCentroids with prior probabilties o Fixed bug in OPLS with proper scaling of data matrices during prediction CHANGES IN Version 0.8.2 [2014-7-23] ------------------------------------ SIGNIFICANT USER-VISIBLE CHANGES o Added 'peakFilter' method o Minor fixes to documentation CHANGES IN Version 0.8.1 [2014-7-10] ------------------------------------ SIGNIFICANT USER-VISIBLE CHANGES o Changed 'parameters' argument to 'model' for ResultSet plot and image o Added 'auto.key' to plot and image for when 'groups' are specified o Added strip labels to plot and image when using base graphics o Added 'coregister' method for 'SpatialShrunkenCentroids' o Method 'image' is now vectorized for argument 'mz' o Method 'plot' is now vectorized for argument 'coord' BUG FIXES o Fixed a bug where conditions are plotted in an incorrect order CHANGES IN Version 0.8.0 [2014-6-16] ------------------------------------ SIGNIFICANT USER-VISIBLE CHANGES o First public beta available for ASMS 2014. CHANGES IN Version 0.7 [2014-6-2] --------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Refactored version of the package prepared for internal testing. o New processing methods, renamed to 'normalize', 'smoothSignal', 'reduceBaseline', 'peakPick', 'peakAlign', 'reduceDimension'. o New function 'readMSIData' for reading supported formats. o Native support for imzML added (no longer requires Java). o Methods 'pixels' and 'features' replaced with updated versions. o In 'features' method, m/z matching now done using bisection search. o New analysis method, renamed to spatialShrunkenCentroids. o Analysis methods now return a new class: 'ResultSet'. o New method 'select' to replace 'selectROI' and 'selectPixels'. CHANGES IN Version 0.6 [2013-2-19] ---------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Major revision to use Bioconductor base packages. o New dependencies on BiocGenerics and Biobase. o New virtual class iSet for generic imaging data. o New classes ImageSet, SImageSet, ImageData, and SImageData. o Revised MSImageSet that uses new parent classes. o New class MIAPE-Imaging for Minimum Information About a Protemics Experiment - Imaging. o New class MSImageProcess for pre-processing information. o Revised functions for importing Analyze 7.5 and imzML o New plotting and image methods using lattice-style formula interface. o New pixelApply and featureApply methods. CHANGES IN Version 0.5 [2013-11-8] ---------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Added image coregistration for 3D sections. o Added 'volume' method for 3D visualization. CHANGES IN Version 0.4 [2013-11-7] ---------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Added 'summaryPlot' method for segmentation visualization. o Exposed 'calibrateSegmentation' method to calibrate colors between multiple MSImageSegmentation objects. o Added more thorough verbose output for 'spatialSparseCluster' and 'spatialSparseKMeans' methods. o Improved behavior of 'intensities' method when reconstructing complex datacubes and with non-contiguous pixel requests. o Changed 'trellisImage' to plot all coordinates for dimensions omitted from 'fixCoord' by default. o Minor changes to the 'MSImageSegmentation' class structure. o Improved 'likPlot' method and added AIC and BIC results and the resulting number of classes. CHANGES IN Version 0.3 [2013-7-5] --------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Improved speed of imaging processing (smoothing and interpolation) methods for use with 'image' and 'trellisImage'. o Added option for verbose output and hooks for GUI progress bars. o For prediction on 'MSImageSegmentation' objects, 'autoDimNames' is now automatically passed along from the original call. o Changed 'MSImageSegmentation' to an S4 class derived from 'list'. o Added option for plotting the probabilities of an 'MSImageSegmentation' using overlaid transparency masks for improved visualization. CHANGES IN Version 0.2 [2013-6-20] ---------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Package renamed from internal code-name "Canary" to "Cardinal". o Split off GUI to a new package called "CardinaliView". o New GUI in "CardinaliView" now based on gWidgets and RGtk2. o Added slot 'peaks' to 'MSImageSet' class. o Changed 'MSPeakFrame' and 'MSPeakList' to S4 classes, and added new class 'MSPeak Alignment'. o Changed how the 'estimateNoise' method estimates noise. o Changed options in the 'detectPeaks' method to be more useful. o Changed the 'alignPeaks' methods to align to the mean spectrum as a reference when aligning a list of peaks. o Added 'interpolate' option for images. o Added new method "selectPeaks" for manual peak selection. o Modified the 'type' arguments in the plotting methods. o Changed 'crossValidate' method to now return predictions for the full dataset for every fold instead of the test set only. BUG FIXES o Fixed bug where plotting mass spectra for multiple pixels fails on datasets with missing mass spectra. o Fixed bug where the 'unload' method did not remove the object. o Fixed bug in the 'crossValidate' method where the dots arguments were not passed to the 'predict' method. CHANGES IN Version 0.1 [2013-6-6] --------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o First internal release for Stanford Canary Center for Cancer Early Detection as primary beta testers. o 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. o 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. o Pre-processing for that includes normalization, baseline correct, peak-picking, peak-alignment, resampling, and binning. o Multivaritate statistical analysis includes PCA, PLS, and OPLS. o Supervised analysis includes a spatially-aware version of nearest shrunken centroids, PLS-DA, and OPLS-DA. o Unsupervised analysis includes spatially-aware clustering based on nearest shrunken centroids, and an implementation based on sparse k-means. o GUI based on tcltk using rpanel that supports all major processing and statistical analysis methods in the package, except for PLS and OPLS.