Merge pull request #10 from maize-genetics/metric-updates

Summary and visualization requests

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rPHG2
 Title: R interface to PHGv2
-Version: 0.5
+Version: 0.6
 Authors@R:
     person(
         given = "Brandon",
@@ -25,7 +25,7 @@ URL:
     https://rphg2.maizegenetics.net/
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Depends: 
     R (>= 4.1.0)
 Imports:

NAMESPACE

@@ -23,11 +23,14 @@ export(metricsIds)
 export(metricsMetaData)
 export(metricsTable)
 export(numberOfChromosomes)
+export(numberOfHaplotypes)
 export(numberOfRefRanges)
-export(numberOfTaxa)
+export(numberOfSamples)
 export(phgType)
 export(plotDot)
 export(plotGvcf)
+export(plotHaploCounts)
+export(plotHaploDist)
 export(port)
 export(readHapIdMetaData)
 export(readHapIdPosMetaData)
@@ -59,11 +62,14 @@ exportMethods(metricsIds)
 exportMethods(metricsMetaData)
 exportMethods(metricsTable)
 exportMethods(numberOfChromosomes)
+exportMethods(numberOfHaplotypes)
 exportMethods(numberOfRefRanges)
-exportMethods(numberOfTaxa)
+exportMethods(numberOfSamples)
 exportMethods(phgType)
 exportMethods(plotDot)
 exportMethods(plotGvcf)
+exportMethods(plotHaploCounts)
+exportMethods(plotHaploDist)
 exportMethods(port)
 exportMethods(readHapIdMetaData)
 exportMethods(readHapIdPosMetaData)

NEWS.md

@@ -1,4 +1,24 @@
-## rPHG 0.5
+## 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

R/class_all_generics.R

@@ -188,6 +188,21 @@ setGeneric("metricsTable<-", function(object, ..., value) standardGeneric("metri
 setGeneric("numberOfChromosomes", function(object, ...) standardGeneric("numberOfChromosomes"))
 
 
+## ----
+#' @title Return number of haplotypes
+#'
+#' @description
+#' Returns the number of haplotypes either for the whole dataset or by each
+#' individual reference range.
+#'
+#' @param object an \code{rPHG2} local or server connection object
+#' @param ... Additional arguments, for use in specific methods
+#'
+#' @rdname numberOfHaplotypes
+#' @export
+setGeneric("numberOfHaplotypes", function(object, ...) standardGeneric("numberOfHaplotypes"))
+
+
 ## ----
 #' @title Return number of reference ranges
 #'
@@ -203,24 +218,25 @@ setGeneric("numberOfRefRanges", function(object, ...) standardGeneric("numberOfR
 
 
 ## ----
-#' @title Return number of taxa
+#' @title Return number of samples
 #'
 #' @description
-#' Returns the number of taxa for a given object
+#' Returns the number of samples for a given object
 #'
 #' @param object an \code{rPHG2} local or server connection object
 #' @param ... Additional arguments, for use in specific methods
 #'
-#' @rdname numberOfTaxa
+#' @rdname numberOfSamples
 #' @export
-setGeneric("numberOfTaxa", function(object, ...) standardGeneric("numberOfTaxa"))
+setGeneric("numberOfSamples", function(object, ...) standardGeneric("numberOfSamples"))
 
 
 ## ----
 #' @title Return type of PHG connection
 #'
 #' @description
-#' Returns the PHG type for a given \code{rPHG2} local or server connection object
+#' Returns the PHG type for a given \code{rPHG2} local or server connection
+#' object
 #'
 #' @param object an \code{rPHG2} connection object
 #' @param ... Additional arguments, for use in specific methods
@@ -258,6 +274,35 @@ setGeneric("plotDot", function(object, ...) standardGeneric("plotDot"))
 setGeneric("plotGvcf", function(object, ...) standardGeneric("plotGvcf"))
 
 
+## ----
+#' @title Plot haplotype counts
+#'
+#' @description
+#' Plots the counts of unique haplotype IDs found in each reference range.
+#'
+#' @param object a \code{\linkS4class{PHGDataSet}} object
+#' @param ... Additional arguments, for use in specific methods
+#'
+#' @rdname plotHaploCounts
+#' @export
+setGeneric("plotHaploCounts", function(object, ...) standardGeneric("plotHaploCounts"))
+
+
+## ----
+#' @title Plot haplotype distribution
+#'
+#' @description
+#' Plots a general distribution of the number of unique haplotypes in a
+#' \code{\linkS4class{PHGDataSet}} object.
+#'
+#' @param object a \code{\linkS4class{PHGDataSet}} object
+#' @param ... Additional arguments, for use in specific methods
+#'
+#' @rdname plotHaploDist
+#' @export
+setGeneric("plotHaploDist", function(object, ...) standardGeneric("plotHaploDist"))
+
+
 ## ----
 #' @title Return port value
 #'

R/class_haplotype_graph.R

@@ -7,7 +7,7 @@
 #'
 #' @slot nChrom Number of chromosomes
 #' @slot nRefRanges Number of reference ranges
-#' @slot nTaxa Number of taxa
+#' @slot nSamples Number of samples
 #' @slot jHapGraph An \code{rJava} \code{jobjRef} object representing a
 #'    \code{HaplotypeGraph} class in the PHG API
 #' @slot jMemAddress An identifier string to the JVM memory space
@@ -20,14 +20,14 @@ setClass(
     slots = c(
         nChrom      = "integer",
         nRefRanges  = "integer",
-        nTaxa       = "integer",
+        nSamples    = "integer",
         jHapGraph   = "jobjRef",
         jMemAddress = "character"
     ),
     prototype = list(
         nChrom      = NA_integer_,
         nRefRanges  = NA_integer_,
-        nTaxa       = NA_integer_,
+        nSamples    = NA_integer_,
         jHapGraph   = rJava::.jnull(),
         jMemAddress = NA_character_
     )
@@ -96,7 +96,7 @@ buildHaplotypeGraph <- function(
         Class       = "HaplotypeGraph",
         nChrom      = jvmGraph$getContigs()$size(),
         nRefRanges  = jvmGraph$numberOfRanges(),
-        nTaxa       = jvmGraph$numberOfSamples(),
+        nSamples    = jvmGraph$numberOfSamples(),
         jHapGraph   = jvmGraph,
         jMemAddress = pointer
     )
@@ -129,9 +129,9 @@ setMethod(
                 "A ", cli::style_bold("HaplotypeGraph"), " object @ ",
                 cli::style_bold(cli::col_blue(javaMemoryAddress(object)))
             ),
-            paste0(" ", pointerSymbol, " # of ref ranges....: ", numberOfRefRanges(object)),
-            paste0(" ", pointerSymbol, " # of taxa..........: ", numberOfTaxa(object)),
-            paste0(" ", pointerSymbol, " # of chromosomes...: ", numberOfChromosomes(object))
+            paste0(" ", pointerSymbol, " # of ref ranges....: ", cli::style_bold(numberOfRefRanges(object))),
+            paste0(" ", pointerSymbol, " # of samples.......: ", cli::style_bold(numberOfSamples(object))),
+            paste0(" ", pointerSymbol, " # of chromosomes...: ", cli::style_bold(numberOfChromosomes(object)))
         )
 
         cat(msg, sep = "\n")
@@ -191,13 +191,13 @@ setMethod(
 
 
 ## ----
-#' @rdname numberOfTaxa
+#' @rdname numberOfSamples
 #' @export
 setMethod(
-    f = "numberOfTaxa",
+    f = "numberOfSamples",
     signature = signature(object = "HaplotypeGraph"),
     definition = function(object) {
-        return(object@nTaxa)
+        return(object@nSamples)
     }
 )