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Changelog

Source: NEWS.md

rPHG2 0.9

  • Added new generic function, findSamplesByHaplotype()
    • Using PHGDataSet objects, users can return all given samples from a provided collection of haplotype IDs.
  • Update seqnames() generic to seqNames():
    • This is to avoid naming collisions in GenomeInfoDb
  • Fixes to possible errors related to ggplot2 v4.0
    • More info can be found here.

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
    • Future plans for integrating TileDB and this release’s AGC interface
  • Fixed plotting bug in plotHaploCounts() geom parameter
  • Added new read* function, readSequence()
    • Returns memory-efficient sequence data from an AGC instance as a Biostrings::DNAString object
    • Can return singlular haplotype sequences or entire reference ranges of sequence data
    • Allows for upstream and downstream padding via the pad parameter
    • This function suite also provides methods of linking a PHGv2 Conda environment to your global R options via the linkCondaBin() function

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:
  • Changed functions and variables containing taxa to samples
  • 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

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