Changelog

Source: NEWS.md

rPHG2 0.8

• Fixed missing IDs returned in readHapIds() method calls.
  • missing values (i.e., "null") now return as NAs in the matrix object
• Removed rlang::abort() condition in initPhg()
  • Now returns “warning” message instead of low-level stop() procedure
• Modified the PHGLocalCon() constructor to now take in either files or a directory path

rPHG2 0.7

• Added new parameter to plotHaploCounts():
  • geom
  • allows user to specify a given geometry (line, bar, or point)
• Added new conditionals for to buildHaplotypeGraph():
  • Checks to see if the JVM is initialized. If not, it will cause an exception and direct user to run initPhg()
• Added new class JvmStats:
  • Returns internal Java and PHG versions and memory information for JVM session
  • Can be instantiated using the jvmStats() constructor function
• Added new checks for initPhg()
• Added new parameters to plotGvcf() function:
  • colorOverride: Overrides bar color based on given user defined color
  • sampleOrder: Overrides default bar ordering based on user defined character vector

rPHG2 0.6

• Added new parameters to plogtGvcf():
  • mData and mVar
  • Allows user to override default sample color option with categorical data
• Added new generic, numberOfHaplotypes():
  • Returns the number of unique haplotypes found within each reference range or the total value found within a PHGDataSet object
• Added getters to PHGDataSet objects:
  • numberOfChromosomes()
  • numberOfSamples()
  • numberOfRefRanges()
• Changed functions and variables containing taxa to samples
  • e.g., numberOfTaxa() is now numberOfSamples()
• Format tweaks to HaplotypeGraph objects’ show() method
• Added new function plotHaploCount():
  • Plots unique haplotype counts for all or given reference ranges
• Added new function plotHaploDist():
  • Plots unique haplotype distribution for entire PHGDataSet object

rPHG2 0.5

• Added new visualization method, plotGvcf():
  • Auto plotting various gVCF metrics
  • Granular metric support through formula subsetting
• Added new accessor and setting method, seqnames()
  • Returns all contig IDs found in a PHGMetrics object
  • Setter version (seqnames()<-) will update old IDs found within a data.frame object
• Added new default methods to plotGvcf() and plotDot() for PHGMetrics objects that only contain one alignment or gVCF dataset

rPHG2 0.4

• Added vignettes and README updates
  • vignette("rPHG2")
• Created build system for website generation
  • rphg2.maizegenetics.net
• Added new class PHGMetrics
  • Primary container for PHGv2 metrics data
• Added accessor methods for PHGMetrics objects:
  • metricsIds()
  • metricsTable()
  • metricsMetaData()
• Prior methods are also updatable
• Added visualization methods:
  • plotDot() - collinearity plotter for alignment data

rPHG2 0.3

• Added new class, PHGDataSet
  • In memory representation of hVCF data sets
• Added new function, filterRefRanges()
  • Filters relevant rPHG2 data objects by reference range
  • Requires a GRanges object as input
• Added new function, filterSamples()
  • Filters relevant rPHG2 data objects by sample ID
  • Input is a basic character vector of sample identifiers

rPHG2 0.2

• Added JVM connections via rJava interface
• Added new class, HaplotypeGraph
  • Wrapper for PHGv2 API Java graph object
• Added new class, PHGLocalCon
  • Interface to local hVCF database and file connections
• Added new function initPHG()
  • Initializes JVM and adds PHGv2 Java JARs to classpath
• Added new function readHapIds()
  • Reads haplotype IDs as a character matrix from a connection object
• Added new function readHapIdMetaData()
  • Reads ALT header metadata for each haplotype ID from a connection object
• Added new function readHapIdPosMetaData()
  • Reads ALT header positional metadata for each haplotype ID from a connection object
• Added new function readSamples()
  • Reads sample IDs from a connection object
• Added new function readRefRanges()
  • Reads reference range positional information as a GRanges object from a connection object