CHANGES IN VERSION 1.7.2
------------------------
* Rebumping the version change with new release of Bioconductor
* Added mean call to the heatmap of vizGenes()
* To combineTCR, filteringMulti now checks to remove list elements with 0 cells.
* Removed top_n() call as it is now deprecated, using slice_max() without ties.
* Add arrange() call during parseTCR() to organize the chains
* Correct the gd flip in the combineContig and subsequent functions
* Removed viridis call in the clonalNetwork() function that was leading to errors
* Matched syntax for strict clonotype in combineBCR()
* Added group.by variable to all applicable visualizations
* Added return.boots to clonalDiversity(), allow for export of all bootstrapped values


CHANGES IN VERSION 1.5.4
------------------------
* modified grabMeta() internal function to no longer assume the active Identity is clusters. 
* checkBlanks() now checks if a blank was detected before trying to remove it
* clonalNetwork() automatically resulted in default error message, bug now removed.
* clonotypeBias now adds z-score of bias when matrix is exported. exportTable parameter is now fixed.

CHANGES IN VERSION 1.5.3
------------------------
* Added loadContigs for non-10X formatted single-cell data
* removed combineTRUST4, superseded by loadContigs
* combineTCR() now allows for > 3 recovered TCRs per barcode
* Readded the filtering steps to combineTCR(), will detect if data is from 10X and automatically remove nonproductive or multi chains. 
* Updated parseTCR() to include evaluation for gamma/delta chains. 

CHANGES IN VERSION 1.5.2
------------------------
* Arbitrarily numbering system to match new bio conductor dev version
* highlightClonotypes() now returns the specific clones instead of clonotype 1, ...
* compareClonotypes numbers parameter now for group-wide numbers and not overall top X numbers
* Fixed issue with clonalDiversity that cause errors when group.by parameter was used. 
* modified parseBCR() to reduce complexity and assume lambda >> kappa
* fixed clusterTCR() function broken with Seurat Objects
* checkContigs no ensures data frames and that "" are converted into NAs
* modified makeGenes() internal function changing na.omit to str_replace_na() and separating the BCR calls by chain to prevent combination errors. 

CHANGES IN VERSION 1.3.5
------------------------
* Modified parseBCR() to check for contents of the chains. Resolve issue with placing light chain into heavy chain slots when 2 contigs are present. 
* Updated checkBlanks to include NA evaluation and placed the check in all .viz functions
* Added clonalNetwork() function
* Modified diversity visualization to remove outliers and place graphs on a single line
* Modified clonalOverlay() to use new internal getCoord() function like clonalNetwork()
* Added threshold parameter to clonesizeDistribution()
* Added support for single-cell objects to clusterTCR()


CHANGES IN VERSION 1.3.4
------------------------
* Modification in clusterTCR() and combineBCR() to speed up the comparison and use less memory
* FilteringMulti, now isolates the top contig by chain, then for barcodes with chains > 2, isolates the top expressing chains. This substantially increases the speed of the filtering step. 
* Modified makeGenes() internal function to use strings str_c()
* Added threshold parameter to combineTRUST4 for B cell manipulation 
* Changed combineTCR function to prevent cell type mix up and clarified in function documentation.
* vizGenes can now be used to look at other component genes of the receptor and "separate" parameter was replaced by "y.axis" parameter.
* Added clonotypeBias() function for inter-cluster comparison.
* Fixed clusterTCR() and combineBCR() assumption that you will have unrelated clones. 


CHANGES IN VERSION 1.3.3
------------------------
* CombineBCR() auto naming function updated to actually name the list elements. 
* Added createHTOContigList() function to create contain list of multiplexed experiments. Fixed issue with groupBy variable
* Added Inv.Pielou matric to diversity call - this is essentially 1-shannon/ln(length). Due to the bootstrapping the length with be constant.
* Added include.na and split.by to occupiedscRepertoire and changed labeling depending on frequency vs proportion
* Added support for single-cell objects for most visualizations, list organizing by single-cell object can be called using split.by variable
* All group and groupBy parameters are now group.by.


CHANGES IN VERSION 1.3.2
------------------------
# This is the new numbering scheme apologies - we are all up-to-date now and now cell ranger >= 5 will # work on bioconductor, so let's all just take that as a win.

* added dot.size parameter to scatterClonotype
* filteringMulti now subsets clonotypes with contains >=2, to prevent 2 of the same chains
* changed how coldata is added to SCE objects using merge instead of union
* Can now add BCR and TCR simultaneously by making large list
* scatter plotting code is not so ugly and allows for user to select dot.size as a variable on the x or y axis
* Removed regressClonotype function - too many dependencies required, adding an additional vignette to go through the process
* Added chain option to visualizations and combineExpression to allow users to facilitate single chains - removed chain option from combineTCR/BCR/TRUST4 (the combined object will have both chains no matter what)
* Added NA filter to combineTCR/BCR/TRUST4 for cell barcodes with only NA values
* Added NA filter to expression2List() for cells with NA clonotypes.
* Updated VizGene to order the genes automatically by highest to lowest variance
* Updated VizGene to pull the correct genes based on selection
* Updated parse method - old version had issue with place V-->J-->D in the TRB/Heavy chains 
* Simplified the clonalDiversity() to allow for more options in organizing plot and box plots. 
* CombineExpression() adds the groupBy variable to Frequency, allowing for multiple calculations to be saved in the meta data. 
* Default color scheme now uses viridis plasma, because it I am on transfusion medicine.

CHANGES IN VERSION 1.2.2
------------------------

# Working on renumbering versions for consistency - this is the new current dev branch
# The below have not been implemented into the master branch or the bioconductor version

* added the combineTRUST4 function to parse contigs from TUST4 pipeline
* added the filter of contigs by chain in the combineTCR, combineBCR, and combineTRUST4 functions
* no longer require the ID in the combineTCR/BCR/TRUST4 functions
* added jaccard index for overlap analysis
* replaced vizVgene with vizGene - allowing users to look at any gene in the combinedContig object
* Fixed coloring scale on the overlap analysis
* Added regressClonotype function using harmony to remove the clonotype effect on feature space
* allowed occupiedRepertoire to use proportion.
* added scatterClonotype function to Viz.R

CHANGES IN VERSION 1.2.1
------------------------

* number of changes to the parseTCR/BCR functions to limit assumptions
* Changed grabMeta to include assessment of colnames
* fixed lengthDF handling of single chains with multi chains stored - ;
* Added labels to alluvialClonotype and occupiedClonotype plotting

CHANGES IN VERSION 1.1.4
------------------------

* replaced hammingCompare with lvCompare to enable superior clonotype calling in combineBCR function.
* added proportion to combineExpression() function so users no longer need to know absolute frequencies when combining the contiguous information. 
* added clusterTCR() and clonalOverlay() functions.
* added downsampling to the diversity calculations
* replaced hammingCompare with lvCompare to enable superior clonotype calling in combineBCR function.
* added proportion to combineExpression() function so users no longer need to know absolute frequencies when combining the contiguous information. 
* added clusterTCR() and clonalOverlay() functions.
* added downsampling to the diversity calculations
* Clonal Overlap Coefficient issue fixed, was comparing unique barcodes and not clonotypes
* Added function checkBlanks to remove list elements without clonotypes, this prevents errors for visualizations
* Re-added Startrac metrics by stripping down the package and adding it piecemeal
* Heavily modified dependencies to reduce total number 

CHANGES IN VERSION 1.0.0
------------------------

* removed dependencies ggfittext and ggdendrogram
* clonesizeDistribution now returns a plot() function


CHANGES IN VERSION 0.99.18
------------------------

* Updated author information in the vignette


CHANGES IN VERSION 0.99.17
------------------------

* Updated NEWS formatting
* Edited DESCRIPTION to SingleCellExperiment R package
* Updated information in the vignette


CHANGES IN VERSION 0.99.16
------------------------

* Added getCirclize() 


CHANGES IN VERSION 0.99.15
------------------------

* Modified numerator for index function


CHANGES IN VERSION 0.99.14
------------------------

* Removed bracket from indexing function

CHANGES IN VERSION 0.99.13
------------------------

* Added exportTable to remaining viz functions
* Modified morisita index to correct error

CHANGES IN VERSION 0.99.12
------------------------

* Reducing the size of the screp_example to fulfill < 5 mB requirement. Randomly samples 100 cells and removed RNA counts from Seurat object

CHANGES IN VERSION 0.99.11
------------------------

* Updated compareClonotype to allow for clonotype comparisons


CHANGES IN VERSION 0.99.10
------------------------

* Bioconductor did not detect the version update.

CHANGES IN VERSION 0.99.9
------------------------

* Bioconductor had no love - changed the Seurat package to imports instead of required, see if that will address the compiling issue that results in a killed: 9 error. 

CHANGES IN VERSION 0.99.8
------------------------

* Passed checks on system, let's see how much bioconductor hates it

CHANGES IN VERSION 0.99.7
------------------------

* But really this time, changed the colData import

CHANGES IN VERSION 0.99.6
------------------------

* Changed colData import

CHANGES IN VERSION 0.99.5
------------------------

* Added screp_example data to package
* Added visVgene function for visualizing the distribution of V genes in TCR
* Added support for monocle to combineExpression function
* Updated documentation for combineTCR() and combineBCR()
* Updated documentation to utilize SingleCellExperiment formats
* Updated Vignette to utilize SingleCellExperiment formats
* Added Author information to vignette
* Add intro and conclusion to vignette
* Removed html knitted vignette
* Removed descriptive code snippets

CHANGES IN VERSION 0.99.4
------------------------

* Modified expression2List() to allow for variables across meta data

CHANGES IN VERSION 0.99.1
------------------------

* Changed R (>= 3.6) to R (>= 4.0)


CHANGES IN VERSION 0.99.0
------------------------

* Changed DESCRIPTION version to 0.99.0
* Removed file seurat_example.rda, accidentally committed
* Deleted git attributes
* reduced Seurat object size for alluvialClonotype in vignette
* Changed the alluvialClonotype assessment to account for only 1 condition


CHANGES IN VERSION 1.2.3
------------------------

* Changed the access of the sample data to github.io repo:
readRDS(url("https://ncborcherding.github.io/vignettes/scRepertoire_example.rds"))


CHANGES IN VERSION 1.2.2
------------------------

* Removed Startrac-based functions in order to pass build on Bioconductor.

DEPRECATED AND DEFUNCT

* Deprecate StartracDiversity()


CHANGES IN VERSION 1.2.0
------------------------

The first version of scRepertoire submitted to Bioconductor.

SIGNIFICANT USER-VISIBLE CHANGES

* Added support for SingleCellExperiement format.


DEPRECATED AND DEFUNCT

* Deprecate combineSeurat in favor or combineExpression().
* Deprecate seurat2List in favor of expression2List().
