NEWS.md

In maize-genetics/rPHG: R front-end for the practical haplotype graph

rPHG 0.2.3

• Fixed issue with variable evaluation in the plotDot() function

rPHG 0.2.2

• Fixed issue with DEMO method endpoint returning incorrect dimensional data for specific Maize PHGv1 methods

rPHG 0.2.1

• Added new function, plotDot()
• Creates dot plots from .anchorspro files
• Added new function, gvcfMetrics()
• Creates summary metrics for a directory of gVCF files

rPHG 0.2.0

• Unified workflow for both local and server instances
• Added new class, PHGServerCon
• New object for connecting to remote public PHG servers using BrAPI endpoints
• Added new class, PHGLocalCon
• New object for connecting to local SQLite or PostgreSQL database instances
• Added new class, HaplotypeGraph
• Wrapper for PHG API Java graph object
• Prior objects now use method dispatch for singular set of methods to return relevant PHG data:
• PHGMethod()
• showPHGMethods()
• readSamples()
• readRefRanges()
• readHaplotypeIds()
• readPHGDataSet()
• Updated summary methods:
• numHaploPerRefRange()
• calcMutualInfo()
• plotGraph()
• plotMutualInfo()

rPHG 0.1.18

• Modified availablePHGMethods():
• Now returns only method IDs for graphs with more than 100 samples in the data
• This prevents publicly available testing methods to be displayed for new PHG users.

rPHG 0.1.17

• Added new "DEMO" method parameter for PHGMethod() constructor:
• specified as PHGMethod("DEMO")
• Will download a small section (25 samples x 1000 reference ranges) of the Goodman/Buckler path data
• Useful for testing and demonstrations

rPHG 0.1.16

• Added new function, plotGraph()
• Returns a visNetwork object for a given section of PHG data filtered by reference range
• Updated installation information on README

rPHG 0.1.15

• Added new function, taxaByNode()
• Returns a tibble object of taxa IDs that are found in a group of haplotype IDs for a given set of reference range IDs
• Update to latest jar files including PHG build

rPHG 0.1.14

• Update logging function (startLogger())
• Add new tests to expand code coverage
• Deprecate BrAPI calls that use external khttp client in PHG jar

rPHG 0.1.13

• Update to latest jar files including PHG build

rPHG 0.1.12

• Added BrAPI endpoint methods for obtaining PHG data from BrAPI webservices:
• BrapiCon
• BrapiConPHG
• readRefRanges()
• readSamples()
• readTable()
• readPHGDatasetFromBrapi()
• filterRefRanges()
• filterSamples()
• serverInfo()
• availablePHGMethods()
• Added Kotlin methods for improved data parsing speeds.
• Added new parameters in graphBuilder()
• buildType - do you want the graph built from paths or haplotypes?

rPHG 0.1.11

• Added NEWS file for tracking version updates.
• Added error checks for catching C stack usage errors for configuration file checks in functions that require configuration file path parameters.
• Fixed edge cases in plotNumHaplo() and plotMutualInfo().

maize-genetics/rPHG documentation built on Feb. 27, 2025, 3:02 a.m.