Merge pull request #5 from maize-genetics/phg-metrics

Add PHG metrics integration

.github/workflows/check-standard.yaml

@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macos-latest,   r: 'release'}
+          # - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,  r: 'release'}
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rPHG2
 Title: R interface to PHGv2
-Version: 0.3.1
+Version: 0.4
 Authors@R:
     person(
         given = "Brandon",
@@ -32,12 +32,16 @@ Imports:
     cli,
     curl,
     GenomicRanges,
+    ggplot2,
     httr,
     IRanges,
     jsonlite,
     methods,
     rJava,
-    tibble
+    rlang,
+    tibble,
+    tools,
+    utils
 VignetteBuilder: knitr
 Suggests:
     knitr,

NAMESPACE

@@ -1,7 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(.DollarNames,PHGMetrics)
+export("%T%")
+export("metricsIds<-")
+export("metricsTable<-")
 export(PHGDataSet)
 export(PHGLocalCon)
+export(PHGMetrics)
 export(PHGServerCon)
 export(brapiURL)
 export(brapiVersion)
@@ -14,10 +19,14 @@ export(httProtocol)
 export(initPhg)
 export(javaMemoryAddress)
 export(javaRefObj)
+export(metricsIds)
+export(metricsMetaData)
+export(metricsTable)
 export(numberOfChromosomes)
 export(numberOfRefRanges)
 export(numberOfTaxa)
 export(phgType)
+export(plotDot)
 export(port)
 export(readHapIdMetaData)
 export(readHapIdPosMetaData)
@@ -30,7 +39,11 @@ exportClasses(HaplotypeGraph)
 exportClasses(PHGCon)
 exportClasses(PHGDataSet)
 exportClasses(PHGLocalCon)
+exportClasses(PHGMetrics)
 exportClasses(PHGServerCon)
+exportMethods("$")
+exportMethods("metricsIds<-")
+exportMethods("metricsTable<-")
 exportMethods(brapiURL)
 exportMethods(brapiVersion)
 exportMethods(filterRefRanges)
@@ -40,10 +53,14 @@ exportMethods(host)
 exportMethods(httProtocol)
 exportMethods(javaMemoryAddress)
 exportMethods(javaRefObj)
+exportMethods(metricsIds)
+exportMethods(metricsMetaData)
+exportMethods(metricsTable)
 exportMethods(numberOfChromosomes)
 exportMethods(numberOfRefRanges)
 exportMethods(numberOfTaxa)
 exportMethods(phgType)
+exportMethods(plotDot)
 exportMethods(port)
 exportMethods(readHapIdMetaData)
 exportMethods(readHapIdPosMetaData)
@@ -54,3 +71,4 @@ exportMethods(readSamples)
 exportMethods(serverInfo)
 importFrom(curl,has_internet)
 importFrom(methods,is)
+importFrom(utils,.DollarNames)

NEWS.md

@@ -3,6 +3,15 @@
   + `vignette("rPHG2")`
 * Created build system for website generation
   + [rphg2.maizegenetics.net](https://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

R/class_all_generics.R

@@ -4,7 +4,7 @@
 #' @description
 #' Returns the Uniform Resource Locator (URL) of a \code{BrapiCon} object.
 #'
-#' @param object an \code{rPHG} local or server connection object.
+#' @param object an \code{rPHG2} local or server connection object.
 #' @param ... Additional arguments, for use in specific methods
 #'
 #' @rdname brapiURL
@@ -18,7 +18,7 @@ setGeneric("brapiURL", function(object, ...) standardGeneric("brapiURL"))
 #' @description
 #' Returns the version ID for a BrAPI-compliant PHG server
 #'
-#' @param object an \code{rPHG} local or server connection object
+#' @param object an \code{rPHG2} local or server connection object
 #' @param ... Additional arguments, for use in specific methods
 #'
 #' @rdname brapiVersion
@@ -30,9 +30,9 @@ setGeneric("brapiVersion", function(object, ...) standardGeneric("brapiVersion")
 #' @title Filter data by reference range
 #'
 #' @description
-#' Filters \code{rPHG}-related datasets by reference range coordinates or ID.
+#' Filters \code{rPHG2}-related datasets by reference range coordinates or ID.
 #'
-#' @param object an \code{rPHG} dataset
+#' @param object an \code{rPHG2} dataset
 #' @param ... Additional arguments, for use in specific methods
 #'
 #' @rdname filterRefRanges
@@ -44,9 +44,9 @@ setGeneric("filterRefRanges", function(object, ...) standardGeneric("filterRefRa
 #' @title Filter data by sample IDs
 #'
 #' @description
-#' Filters \code{rPHG}-related datasets by sample ID.
+#' Filters \code{rPHG2}-related datasets by sample ID.
 #'
-#' @param object an \code{rPHG} dataset
+#' @param object an \code{rPHG2} dataset
 #' @param ... Additional arguments, for use in specific methods
 #'
 #' @rdname filterSamples
@@ -60,7 +60,7 @@ setGeneric("filterSamples", function(object, ...) standardGeneric("filterSamples
 #' @description
 #' Returns the host information for a given object
 #'
-#' @param object an \code{rPHG} local or server connection object
+#' @param object an \code{rPHG2} local or server connection object
 #' @param ... Additional arguments, for use in specific methods
 #'
 #' @rdname host
@@ -74,7 +74,7 @@ setGeneric("host", function(object, ...) standardGeneric("host"))
 #' @description
 #' Returns the protocol information for a given object
 #'
-#' @param object an \code{rPHG} local or server connection object
+#' @param object an \code{rPHG2} local or server connection object
 #' @param ... Additional arguments, for use in specific methods
 #'
 #' @rdname httProtocol
@@ -88,7 +88,7 @@ setGeneric("httProtocol", function(object, ...) standardGeneric("httProtocol"))
 #' @description
 #' Returns a list of hVCF files.
 #'
-#' @param object an \code{rPHG} local connection object
+#' @param object an \code{rPHG2} local connection object
 #' @param ... Additional arguments, for use in specific methods
 #'
 #' @rdname hVcfFiles
@@ -100,9 +100,9 @@ setGeneric("hVcfFiles", function(object, ...) standardGeneric("hVcfFiles"))
 #' @title Return \code{rJava} reference object
 #'
 #' @description
-#' Returns the \code{rJava} memory reference for a given \code{rPHG} object
+#' Returns the \code{rJava} memory reference for a given \code{rPHG2} object
 #'
-#' @param object an \code{rPHG} local or server connection object
+#' @param object an \code{rPHG2} local or server connection object
 #' @param ... Additional arguments, for use in specific methods
 #'
 #' @rdname javaMemoryAddress
@@ -114,23 +114,73 @@ setGeneric("javaMemoryAddress", function(object, ...) standardGeneric("javaMemor
 #' @title Return \code{rJava} reference object
 #'
 #' @description
-#' Returns the \code{rJava} memory reference for a given \code{rPHG} object
+#' Returns the \code{rJava} memory reference for a given \code{rPHG2} object
 #'
-#' @param object an \code{rPHG} local or server connection object
+#' @param object an \code{rPHG2} local or server connection object
 #' @param ... Additional arguments, for use in specific methods
 #'
 #' @rdname javaRefObj
 #' @export
 setGeneric("javaRefObj", function(object, ...) standardGeneric("javaRefObj"))
 
 
+## ----
+#' @title Return metrics table IDs
+#'
+#' @description
+#' Returns a PHG metrics table by given ID
+#'
+#' @param object an \code{rPHG2} metrics object
+#' @param ... Additional arguments, for use in specific methods
+#'
+#' @rdname metricsIds
+#' @export
+setGeneric("metricsIds", function(object, ...) standardGeneric("metricsIds"))
+
+#' @rdname metricsIds
+#' @export
+setGeneric("metricsIds<-", function(object, ..., value) standardGeneric("metricsIds<-"))
+
+
+## ----
+#' @title Return metric metadata
+#'
+#' @description
+#' Returns metadata information from \code{rPHG2} metrics objects
+#'
+#' @param object an \code{rPHG2} metrics object
+#' @param ... Additional arguments, for use in specific methods
+#'
+#' @rdname metricsMetaData
+#' @export
+setGeneric("metricsMetaData", function(object, ...) standardGeneric("metricsMetaData"))
+
+
+## ----
+#' @title Return a metrics table
+#'
+#' @description
+#' Returns a PHG metrics table by given ID
+#'
+#' @param object an \code{rPHG2} metrics object
+#' @param ... Additional arguments, for use in specific methods
+#'
+#' @rdname metricsTable
+#' @export
+setGeneric("metricsTable", function(object, ...) standardGeneric("metricsTable"))
+
+#' @rdname metricsTable
+#' @export
+setGeneric("metricsTable<-", function(object, ..., value) standardGeneric("metricsTable<-"))
+
+
 ## ----
 #' @title Return number of chromosomes
 #'
 #' @description
 #' Returns the number of chromosomes for a given object
 #'
-#' @param object an \code{rPHG} local or server connection object
+#' @param object an \code{rPHG2} local or server connection object
 #' @param ... Additional arguments, for use in specific methods
 #'
 #' @rdname numberOfChromosomes
@@ -144,7 +194,7 @@ setGeneric("numberOfChromosomes", function(object, ...) standardGeneric("numberO
 #' @description
 #' Returns the number of reference ranges for a given object
 #'
-#' @param object an \code{rPHG} local or server connection object
+#' @param object an \code{rPHG2} local or server connection object
 #' @param ... Additional arguments, for use in specific methods
 #'
 #' @rdname numberOfRefRanges
@@ -158,7 +208,7 @@ setGeneric("numberOfRefRanges", function(object, ...) standardGeneric("numberOfR
 #' @description
 #' Returns the number of taxa for a given object
 #'
-#' @param object an \code{rPHG} local or server connection object
+#' @param object an \code{rPHG2} local or server connection object
 #' @param ... Additional arguments, for use in specific methods
 #'
 #' @rdname numberOfTaxa
@@ -170,23 +220,37 @@ setGeneric("numberOfTaxa", function(object, ...) standardGeneric("numberOfTaxa")
 #' @title Return type of PHG connection
 #'
 #' @description
-#' Returns the PHG type for a given \code{rPHG} local or server connection object
+#' Returns the PHG type for a given \code{rPHG2} local or server connection object
 #'
-#' @param object an \code{rPHG} connection object
+#' @param object an \code{rPHG2} connection object
 #' @param ... Additional arguments, for use in specific methods
 #'
 #' @rdname phgType
 #' @export
 setGeneric("phgType", function(object, ...) standardGeneric("phgType"))
 
 
+## ----
+#' @title Generate dot plots
+#'
+#' @description
+#' Generates collinearity (dot) plots between 2 samples
+#'
+#' @param object an \code{rPHG2} metrics object
+#' @param ... Additional arguments, for use in specific methods
+#'
+#' @rdname plotDot
+#' @export
+setGeneric("plotDot", function(object, ...) standardGeneric("plotDot"))
+
+
 ## ----
 #' @title Return port value
 #'
 #' @description
 #' Returns the port information for a given object
 #'
-#' @param object an \code{rPHG} local or server connection object
+#' @param object an \code{rPHG2} local or server connection object
 #' @param ... Additional arguments, for use in specific methods
 #'
 #' @rdname port
@@ -201,7 +265,7 @@ setGeneric("port", function(object, ...) standardGeneric("port"))
 #' Gets haplotype ID for given samples and reference ranges from a
 #' \code{HaplotypeGraph}
 #'
-#' @param object an \code{rPHG} local or server connection object
+#' @param object an \code{rPHG2} local or server connection object
 # @param nThreads Number of threads to use when evaluating haplotype IDs
 #' @param ... Additional arguments, for use in specific methods
 #'
@@ -217,7 +281,7 @@ setGeneric("readHapIds", function(object, ...) standardGeneric("readHapIds"))
 #' Gets haplotype ID metadata for given samples and reference ranges from a
 #' \code{HaplotypeGraph}
 #'
-#' @param object an \code{rPHG} local or server connection object
+#' @param object an \code{rPHG2} local or server connection object
 #' @param ... Additional arguments, for use in specific methods
 #'
 #' @rdname readHapIdMetaData
@@ -232,7 +296,7 @@ setGeneric("readHapIdMetaData", function(object, ...) standardGeneric("readHapId
 #' Gets haplotype ID positional metadata for given samples and reference ranges
 #' from a \code{HaplotypeGraph}
 #'
-#' @param object an \code{rPHG} local or server connection object
+#' @param object an \code{rPHG2} local or server connection object
 #' @param ... Additional arguments, for use in specific methods
 #'
 #' @rdname readHapIdPosMetaData
@@ -247,7 +311,7 @@ setGeneric("readHapIdPosMetaData", function(object, ...) standardGeneric("readHa
 #' Returns all haplotype, sample, and reference range IDs and relative metadata
 #' from a \code{\linkS4class{HaplotypeGraph}} object.
 #'
-#' @param object an \code{rPHG} local or server connection object
+#' @param object an \code{rPHG2} local or server connection object
 #' @param ... Additional arguments, for use in specific methods
 #'
 #' @rdname readPhgDataSet
@@ -261,7 +325,7 @@ setGeneric("readPhgDataSet", function(object, ...) standardGeneric("readPhgDataS
 #' @description
 #' Get reference range data from a \code{HaplotypeGraph}
 #'
-#' @param object an \code{rPHG} local or server connection object
+#' @param object an \code{rPHG2} local or server connection object
 #' @param ... Additional arguments, for use in specific methods
 #'
 #' @rdname readRefRanges
@@ -275,7 +339,7 @@ setGeneric("readRefRanges", function(object, ...) standardGeneric("readRefRanges
 #' @description
 #' Gets sample ID data from a \code{HaplotypeGraph}
 #'
-#' @param object an \code{rPHG} local or server connection object
+#' @param object an \code{rPHG2} local or server connection object
 #' @param ... Additional arguments, for use in specific methods
 #'
 #' @rdname readSamples
@@ -289,7 +353,7 @@ setGeneric("readSamples", function(object, ...) standardGeneric("readSamples"))
 #' @description
 #' Get available BrAPI calls from BrAPI compliant PHG server
 #'
-#' @param object an \code{rPHG} local or server connection object
+#' @param object an \code{rPHG2} local or server connection object
 #' @param ... Additional arguments, for use in specific methods
 #'
 #' @rdname serverInfo