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rPHG2 0.7
- Added new parameter to
plotHaploCounts()
:
geom
- allows user to specify a given geometry (line, bar, or point)
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
- Added vignettes and README updates
- Created build system for website generation
- Added new class
PHGMetrics
- Primary container for PHGv2 metrics data
- Added accessor methods for
PHGMetrics
objects:
- 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()
- Read reference range positional information as a
GRanges
object from a connection object