Merge pull request #11 from maize-genetics/doc-fix

Add `geom` parameter to `plotHaploCounts()`

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rPHG2
 Title: R interface to PHGv2
-Version: 0.6
+Version: 0.6.1
 Authors@R:
     person(
         given = "Brandon",
@@ -41,6 +41,7 @@ Imports:
     patchwork,
     rJava,
     rlang,
+    S4Vectors,
     scales,
     tibble,
     tools,

NEWS.md

@@ -1,3 +1,9 @@
+## 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`

R/class_phg_dataset.R

@@ -228,75 +228,42 @@ setMethod(
 
 ## ----
 #' @param gr
-#' A \code{GenomicRanges} object for subsetting based on chromosome ID and
-#' start/stop positions (bp). If \code{NULL}, all haplotype counts will be
-#' plotted similar to a Manhattan plot. Defaults to \code{NULL}.
+#' A \code{GRanges} object specifying a genomic range for filtering the
+#' haplotype data. If \code{NULL}, the function will plot the data across the
+#' entire dataset.
+#' @param geom
+#' A character string specifying the type of geometric representation for the
+#' plot. Accepted values are:
+#' \itemize{
+#'   \item \code{"l"} for lines (default),
+#'   \item \code{"b"} for bars,
+#'   \item \code{"p"} for points.
+#' }
+#' If an invalid value is provided, the function will raise an error.
+#'
+#' @details
+#' When no genomic range is provided (i.e., \code{gr = NULL}), the function
+#' plots the number of unique haplotypes across the entire reference genome or
+#' dataset. This will default to point geometry regardless of the value
+#' provided within the \code{geom} parameter. If a genomic range is provided,
+#' it filters the data based on overlaps between the reference ranges in the
+#' dataset and the query range. In both cases, the resulting plot uses
+#' \code{ggplot2} for visualization, and different geometries can be selected
+#' via the \code{geom} parameter.
+#'
+#' @return A \code{ggplot} object visualizing the haplotype counts. When
+#' \code{gr} is \code{NULL}, the plot shows the number of unique haplotypes
+#' across reference positions. When \code{gr} is provided, the plot is filtered
+#' to display haplotype counts within the specified range.
+#'
 #'
 #' @rdname plotHaploCounts
 #' @export
 setMethod(
     f = "plotHaploCounts",
     signature = signature(object = "PHGDataSet"),
-    definition = function(object, gr = NULL) {
-        nHaplo <- numberOfHaplotypes(object, byRefRange = TRUE)
-        p <- NULL
-        if (is.null(gr)) {
-            p <- ggplot2::ggplot(nHaplo) +
-                ggplot2::aes(x = !!rlang::sym("start"), y = !!rlang::sym("n_haplo")) +
-                ggplot2::geom_point() +
-                ggplot2::scale_y_continuous(
-                    breaks = seq_len(max(nHaplo$n_haplo)),
-                    limits = c(1, max(nHaplo$n_haplo))
-                ) +
-                ggplot2::scale_x_continuous(
-                    labels = scales::label_number(
-                        scale_cut = scales::cut_short_scale()
-                    )
-                ) +
-                ggplot2::xlab("Position (bp)") +
-                ggplot2::ylab("Number of unique haplotypes") +
-                ggplot2::facet_wrap(~ seqnames, scales = "free_x") +
-                ggplot2::theme_bw()
-        } else {
-            refRanges <- readRefRanges(object)
-            if (!is(gr, "GRanges")) {
-                rlang::abort("'gr' object is not of type 'GRanges'")
-            }
-
-            gr$sub_id <- paste0("QR ", GenomeInfoDb::seqnames(gr), ":", IRanges::ranges(gr))
-
-            # Find overlaps
-            overlaps <- suppressWarnings(GenomicRanges::findOverlaps(refRanges, gr))
-            if (length(overlaps) == 0) {
-                rlang::abort("No reference ranges identified with given query")
-            }
-
-            # Filter based on overlaps
-            filtGr <- refRanges[S4Vectors::queryHits(overlaps)]
-
-            # Add sub_id metadata
-            filtGr$sub_id <- gr$sub_id[S4Vectors::subjectHits(overlaps)]
-            filtGrDf <- as.data.frame(filtGr)
-            filtGrDf <- merge(x = filtGrDf, y = nHaplo)
-
-            p <- ggplot2::ggplot(filtGrDf) +
-                ggplot2::aes(x = !!rlang::sym("rr_id"), y = !!rlang::sym("n_haplo")) +
-                ggplot2::geom_bar(stat = "identity") +
-                ggplot2::scale_y_continuous(breaks = seq(0, max(nHaplo$n_haplo), by = 1)) +
-                ggplot2::xlab("Reference range ID") +
-                ggplot2::ylab("Number of unique haplotypes") +
-                ggplot2::facet_grid(~ sub_id, scales = "free_x", space = "free") +
-                ggplot2::theme_bw() +
-                ggplot2::theme(
-                    axis.text.x = ggplot2::element_text(
-                        angle = 90,
-                        vjust = 0.5,
-                        hjust = 1
-                    )
-                )
-        }
-
-        return(p)
+    definition = function(object, gr = NULL, geom = "l") {
+        plotHaploFromPhgDataSet(object, gr, geom)
     }
 )
 

R/vis_plot_dot.R

@@ -1,3 +1,4 @@
+## ----
 # Plot a Dot Plot from AnchorWave metrics
 #
 # @param df

R/vis_plot_haplo.R

@@ -0,0 +1,131 @@
+## ----
+# Helper function to construct common ggplot theme
+custHapTheme <- function() {
+    ggplot2::theme_bw() +
+        ggplot2::theme(
+            axis.text.x = ggplot2::element_text(
+                angle = 90,
+                vjust = 0.5,
+                hjust = 1
+            )
+        )
+}
+
+
+## ----
+# Helper function to construct the geometry based on the 'geom' parameter
+selectGeom <- function(geom) {
+    switch(geom,
+           "l" = ggplot2::geom_line(ggplot2::aes(group = 1)),
+           "b" = ggplot2::geom_bar(stat = "identity"),
+           "p" = ggplot2::geom_point()
+    )
+}
+
+
+## ----
+# Plot Haplotype Data from PHG Dataset
+#
+# @description
+# This function creates a ggplot visualization of haplotype data from a PHG
+# (Practical Haplotype Graph) dataset, allowing for multiple geometric
+# representations (lines, bars, points). The plot can either cover the entire
+#  dataset or a specific genomic range provided by the user.
+#
+# @param object
+# A PHG dataset object containing haplotype information. This is typically the
+# output of a function like `loadPhgDataSet()` or similar.
+# @param gr
+# A \code{GRanges} object specifying a genomic range for filtering the
+# haplotype data. If \code{NULL}, the function will plot the data across the
+# entire dataset.
+# @param geom
+# A character string specifying the type of geometric representation for the
+# plot. Accepted values are:
+# \itemize{
+#   \item \code{"l"} for lines (default),
+#   \item \code{"b"} for bars,
+#   \item \code{"p"} for points.
+# }
+# If an invalid value is provided, the function will raise an error.
+#
+# @details
+# When no genomic range is provided (i.e., \code{gr = NULL}), the function
+# plots the number of unique haplotypes across the entire reference genome or
+# dataset. If a genomic range is provided, it filters the data based on
+# overlaps between the reference ranges in the dataset and the query range. In
+# both cases, the resulting plot uses \code{ggplot2} for visualization, and
+# different geometries can be selected via the \code{geom} parameter.
+#
+# @return A \code{ggplot} object visualizing the haplotype counts. When
+# \code{gr} is \code{NULL}, the plot shows the number of unique haplotypes
+# across reference positions. When \code{gr} is provided, the plot is filtered
+# to display haplotype counts within the specified range.
+plotHaploFromPhgDataSet <- function(object, gr = NULL, geom = "l") {
+    # Validate 'geom' parameter
+    if (!geom %in% c("l", "b", "p")) {
+        rlang::abort("'geom' must be one of 'l' (line), 'b' (bar), or 'p' (point).")
+    }
+
+    nHaplo <- numberOfHaplotypes(object, byRefRange = TRUE)
+
+    # Plot when 'gr' is NULL
+    if (is.null(gr)) {
+        return(
+            ggplot2::ggplot(nHaplo) +
+                ggplot2::aes(
+                    x = !!rlang::sym("start"),
+                    y = !!rlang::sym("n_haplo"),
+                    alpha = 0.01
+                ) +
+                selectGeom("p") +
+                ggplot2::scale_y_continuous(
+                    breaks = seq_len(max(nHaplo$n_haplo)),
+                    limits = c(1, max(nHaplo$n_haplo))
+                ) +
+                ggplot2::scale_x_continuous(
+                    labels = scales::label_number(
+                        scale_cut = scales::cut_short_scale()
+                    )
+                ) +
+                ggplot2::xlab("Position (bp)") +
+                ggplot2::ylab("Number of unique haplotypes") +
+                ggplot2::facet_wrap(~ seqnames, scales = "free_x") +
+                ggplot2::guides(alpha = "none") +
+                custHapTheme()
+        )
+    }
+
+    # Validate 'gr' type
+    if (!is(gr, "GRanges")) {
+        rlang::abort("'gr' object is not of type 'GRanges'")
+    }
+
+    # Get ref ranges GRanges object and add 'sub_id" parameters
+    refRanges <- readRefRanges(object)
+    gr$sub_id <- paste0("QR ", GenomeInfoDb::seqnames(gr), ":", IRanges::ranges(gr))
+
+    # Find overlaps
+    overlaps <- suppressWarnings(GenomicRanges::findOverlaps(refRanges, gr))
+
+    if (length(overlaps) == 0) {
+        rlang::abort("No reference ranges identified with given query")
+    }
+
+    # Filter and merge data
+    filtGr <- refRanges[S4Vectors::queryHits(overlaps)]
+    filtGr$sub_id <- gr$sub_id[S4Vectors::subjectHits(overlaps)]
+    filtGrDf <- merge(as.data.frame(filtGr), nHaplo)
+
+    # Plot with filtered data
+    ggplot2::ggplot(filtGrDf) +
+        ggplot2::aes(x = !!rlang::sym("rr_id"), y = !!rlang::sym("n_haplo")) +
+        selectGeom(geom) +
+        ggplot2::scale_y_continuous(breaks = seq(0, max(nHaplo$n_haplo), by = 1)) +
+        ggplot2::xlab("Reference range ID") +
+        ggplot2::ylab("Number of unique haplotypes") +
+        ggplot2::facet_grid(~ sub_id, scales = "free_x", space = "free") +
+        custHapTheme()
+}
+
+

tests/testthat/test_class_phg_dataset.R

@@ -69,9 +69,31 @@ test_that("PHGDataSet class construction tests", {
     ### expect 4 observations to overlap with successful query
     expect_equal(length(testPlot$data$rr_id), 4)
 
+    ## Geometry ('geom = ') tests
+    containsGeom <- function(plot, geomType) {
+        any(
+            sapply(plot$layers, function(layer) {
+                inherits(layer$geom, geomType)
+            })
+        )
+    }
+    expect_true(containsGeom(plotHaploCounts(pds, geom = "p"), "GeomPoint"))
+    expect_true(containsGeom(plotHaploCounts(pds, geom = "l"), "GeomPoint"))
+    expect_true(containsGeom(plotHaploCounts(pds, geom = "b"), "GeomPoint"))
+    expect_true(containsGeom(plotHaploCounts(pds, gr = grQuery, geom = "l"), "GeomLine"))
+    expect_false(containsGeom(plotHaploCounts(pds, gr = grQuery, geom = "l"), "GeomBar"))
+    expect_false(containsGeom(plotHaploCounts(pds, gr = grQuery, geom = "l"), "GeomPoint"))
+    expect_true(containsGeom(plotHaploCounts(pds, gr = grQuery, geom = "b"), "GeomBar"))
+    expect_false(containsGeom(plotHaploCounts(pds, gr = grQuery, geom = "b"), "GeomLine"))
+    expect_false(containsGeom(plotHaploCounts(pds, gr = grQuery, geom = "b"), "GeomPoint"))
+    expect_true(containsGeom(plotHaploCounts(pds, gr = grQuery, geom = "p"), "GeomPoint"))
+    expect_false(containsGeom(plotHaploCounts(pds, gr = grQuery, geom = "p"), "GeomBar"))
+    expect_false(containsGeom(plotHaploCounts(pds, gr = grQuery, geom = "p"), "GeomLine"))
+
     ## General errors
     expect_error(plotHaploCounts(pds, gr = mtcars))
     expect_error(plotHaploCounts(pds, gr = grQueryError))
+    expect_error(plotHaploCounts(pds, geom = "x"))
 })
 
 

tests/testthat/test_utils_metrics.R

@@ -2,10 +2,13 @@ test_that("General metrics utility tests", {
     # validateHeaders()
     x <- "some\tline\tto\ttest"
     expect_true(
-        rPHG2:::validateHeaders(x, c("some", "line", "to", "test"))
+        validateHeaders(x, c("some", "line", "to", "test"))
     )
     expect_false(
-        rPHG2:::validateHeaders(NULL, c("some", "line", "to", "test"))
+        validateHeaders(NULL, c("some", "line", "to", "test"))
+    )
+    expect_false(
+        validateHeaders(NULL, c("some", "line", "to", "ttest"))
     )
 })