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test-msn.R
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test-msn.R
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ucl <- function(x){
unclass(x$graph)[-10]
}
set.seed(9005)
gend <- new("genind"
, tab = structure(c(1L, 1L, 0L, 0L,
1L, 1L, 2L, 2L,
0L, 1L, 1L, 0L,
2L, 1L, 1L, 2L),
.Dim = c(4L, 4L),
.Dimnames = list(c("1", "2", "3", "4"),
c("loc-1.1", "loc-1.2", "loc-2.1", "loc-2.2")))
, loc.names = structure(c("loc-1", "loc-2"), .Names = c("loc-1", "loc-2"))
, loc.fac = structure(c(1L, 1L, 2L, 2L), .Label = c("loc-1", "loc-2"), class = "factor")
, loc.nall = structure(c(2L, 2L), .Names = c("loc-1", "loc-2"))
, all.names = structure(list(`loc-1` = structure(c("3", "4"), .Names = c("1", "2"
)), `loc-2` = structure(c("3", "4"), .Names = c("1", "2"))), .Names = c("loc-1",
"loc-2"))
, call = NULL
, ind.names = structure(c("", "", "", ""), .Names = c("1", "2", "3", "4"))
, pop = structure(1:4, .Label = c("1", "2", "3", "4"), class = "factor")
, pop.names = structure(c("1", "2", "3", "4"))
, ploidy = 2L
, type = "codom"
, other = NULL
)
gend_gc <- as.genclone(gend)
gend_bruvo <- bruvo.dist(gend, replen = c(1, 1))
gend_single <- gend
pop(gend_single) <- rep("A", 4)
#' Identical population and color fields
#'
#' @param g1 graph 1
#' @param g2 graph 2
#'
#' @noRd
expect_identical_metadata <- function(g1, g2){
eval(bquote(expect_identical(.(g1[-1]), .(g2[-1]))))
}
#' Vertex counts
#'
#' @param g a graph
#' @param n an integer equal to the number of vertices in the graph
#'
#' @noRd
expect_vcount <- function(g, n){
eval(bquote(expect_equal(igraph::vcount(.(g$graph)), .(n))))
}
#' Edge counts
#'
#' @param g a graph
#' @param n an integer equal to the number of edges in the graph
#'
#' @noRd
expect_ecount <- function(g, n){
eval(bquote(expect_equal(igraph::ecount(.(g$graph)), .(n))))
}
#' Identical attributes
#'
#' @param g1 graph 1
#' @param g2 graph 2
#' @param a a character specifying which attribute to test
#'
#' @noRd
expect_identical_vertex_attr <- function(g1, g2, a){
eval(bquote(expect_identical(igraph::vertex_attr(.(g1)$graph, .(a)),
igraph::vertex_attr(.(g2)$graph, .(a))
)
))
}
#' Identical attributes
#'
#' @param g1 graph 1
#' @param g2 graph 2
#' @param a a character specifying which attribute to test
#'
#' @noRd
expect_identical_edge_attr <- function(g1, g2, a){
eval(bquote(expect_identical(igraph::edge_attr(.(g1)$graph, .(a)),
igraph::edge_attr(.(g2)$graph, .(a))
)
))
}
#' Attribute names
#'
#' @param g a graph
#' @param a a character vector specifying all the named attributes
#'
#' @noRd
expect_vertex_attr <- function(g, a){
eval(bquote(expect_equal(igraph::vertex_attr_names(.(g$graph)), .(a))))
}
expect_vertex_size_scale <- function(g, s){
eval(bquote(expect_equal(sort(igraph::vertex_attr(.(g$graph), "size")^2),
sort(.(s)))))
}
#' Testing distance tables
#'
#' @param g a graph
#' @param d a tabulaton of the distances between nodes. For example, a graph
#' with four nodes connected in a line would have 3:1, indicating that there
#' are three pairs that can be reached with one step, two with two steps, and
#' one pair needs three steps.
#'
#' @noRd
expect_distance_table <- function(g, d){
eval(bquote(expect_equal(igraph::distance_table(.(g$graph))$res, .(d))))
}
bruv_no_ties <- bruvo.msn(gend, replen = c(1,1), showplot = FALSE)
bruv_ties <- bruvo.msn(gend, replen = c(1,1), showplot = FALSE, include.ties = TRUE)
pmsn_no_ties <- poppr.msn(gend, distmat = gend_bruvo, showplot = FALSE)
pmsn_ties <- poppr.msn(gend, distmat = gend_bruvo, showplot = FALSE, include.ties = TRUE)
sbruv_no_ties <- bruvo.msn(gend_single, replen = c(1,1), showplot = FALSE)
sbruv_ties <- bruvo.msn(gend_single, replen = c(1,1), showplot = FALSE, include.ties = TRUE)
spmsn_no_ties <- poppr.msn(gend_single, distmat = gend_bruvo, showplot = FALSE)
spmsn_ties <- poppr.msn(gend_single, distmat = gend_bruvo, showplot = FALSE, include.ties = TRUE)
pienames <- c("name", "size", "shape", "pie", "pie.color", "label")
nopienames <- c("name", "size", "color", "label")
context("Input parameter tests")
test_that("{poppr,bruvo}.msn needs a genind object to work", {
expect_error(poppr.msn(1:10), "must be a genind")
expect_error(bruvo.msn(1:10), "must be a genind")
})
test_that("distance matrix must be valid", {
expect_error(poppr.msn(gend, distmat = 1:10),
"The distance matrix is neither a dist object nor a matrix.")
expect_error(poppr.msn(gend, distmat = as.matrix(gend_bruvo)[-1, ]),
"The size of the distance matrix does not match the size of the data.")
})
context("Tied MSN edge tests")
test_that("bruvo.msn can properly account for tied edges", {
# metadata are equal
expect_identical_metadata(bruv_no_ties, bruv_ties)
# There will be four tied edges, but only 3 untied.
expect_ecount(bruv_no_ties, 3L)
expect_ecount(bruv_ties, 4L)
# vertex attributes come with pie
expect_vertex_attr(bruv_no_ties, pienames)
expect_vertex_attr(bruv_ties, pienames)
# both graphs will have the same number of vertices
expect_vcount(bruv_no_ties, 4L)
expect_vcount(bruv_ties, 4L)
# Adding a loop will shrink the distance between nodes 1 and 4
expect_distance_table(bruv_no_ties, 3:1)
expect_distance_table(bruv_ties, c(4, 2))
})
test_that("poppr.msn can properly account for tied edges", {
# metadata are equal
expect_identical_metadata(pmsn_no_ties, pmsn_ties)
# There will be four tied edges, but only 3 untied.
expect_ecount(pmsn_no_ties, 3L)
expect_ecount(pmsn_ties, 4L)
# vertex attributes come with pie
expect_vertex_attr(pmsn_no_ties, pienames)
expect_vertex_attr(pmsn_ties, pienames)
# both graphs will have the same number of vertices
expect_vcount(pmsn_no_ties, 4L)
expect_vcount(pmsn_ties, 4L)
# Adding a loop will shrink the distance between nodes 1 and 4
expect_distance_table(pmsn_no_ties, 3:1)
expect_distance_table(pmsn_ties, c(4, 2))
})
test_that("bruvo.msn can work with single populations", {
# metadata are equal
expect_identical_metadata(sbruv_no_ties, sbruv_ties)
# There will be four tied edges, but only 3 untied.
expect_ecount(sbruv_no_ties, 3L)
expect_ecount(sbruv_ties, 4L)
# both graphs will have the same number of vertices
expect_vcount(sbruv_no_ties, 4L)
expect_vcount(sbruv_ties, 4L)
# vertex attributes don't come with pie :(
expect_vertex_attr(sbruv_no_ties, nopienames)
expect_vertex_attr(sbruv_ties, nopienames)
# Adding a loop will shrink the distance between nodes 1 and 4
expect_distance_table(sbruv_no_ties, 3:1)
expect_distance_table(sbruv_ties, c(4, 2))
})
test_that("poppr.msn can work with single populations", {
# metadata are equal
expect_identical_metadata(spmsn_no_ties, spmsn_ties)
# There will be four tied edges, but only 3 untied.
expect_ecount(spmsn_no_ties, 3L)
expect_ecount(spmsn_ties, 4L)
# vertex attributes don't come with pie :(
expect_vertex_attr(spmsn_no_ties, nopienames)
expect_vertex_attr(spmsn_ties, nopienames)
# both graphs will have the same number of vertices
expect_vcount(spmsn_no_ties, 4L)
expect_vcount(spmsn_ties, 4L)
# Adding a loop will shrink the distance between nodes 1 and 4
expect_distance_table(spmsn_no_ties, 3:1)
expect_distance_table(spmsn_ties, c(4, 2))
})
context("plot_poppr_msn tests")
test_that("plot_poppr_msn needs a genind object up front", {
skip_on_cran()
expect_error(plot_poppr_msn(pmsn_ties, gend), "pmsn_ties is not a genind")
})
test_that("plot_poppr_msn for some reason needs the silly listgraph", {
skip_on_cran()
expect_error(plot_poppr_msn(gend, pmsn_ties$graph), "graph not compatible")
})
test_that("the user can label specific nodes (UX)", {
skip_on_cran()
# Note: this test can really only test that this feature doesn't cause the
# function to break
x <- plot_poppr_msn(gend, pmsn_ties, nodescale = 40, inds = 4)
expect_identical(ucl(x), ucl(pmsn_ties))
x <- plot_poppr_msn(gend, pmsn_ties, nodescale = 40, inds = "4")
expect_identical(ucl(x), ucl(pmsn_ties))
})
test_that("plot_poppr_msn can use layouts", {
skip_on_cran()
x <- plot_poppr_msn(gend, pmsn_ties, layfun = igraph::layout_as_tree)
expect_identical(ucl(x), ucl(pmsn_ties))
})
test_that("plot_poppr_msn will label MLGs (UX)", {
skip_on_cran()
x <- plot_poppr_msn(gend, pmsn_ties, mlg = TRUE)
expect_identical(ucl(x), ucl(pmsn_ties))
})
test_that("plot_poppr_msn will not take the quantiles for the legend (UX)", {
skip_on_cran()
x <- plot_poppr_msn(gend, pmsn_ties, quantiles = FALSE)
expect_identical(ucl(x), ucl(pmsn_ties))
})
test_that("plot_poppr_msn can plot without legends (UX)", {
skip_on_cran()
x <- plot_poppr_msn(gend, pmsn_ties, pop.leg = FALSE, size.leg = FALSE, scale.leg = FALSE)
expect_identical(ucl(x), ucl(pmsn_ties))
x <- plot_poppr_msn(gend, pmsn_ties, pop.leg = TRUE, size.leg = FALSE, scale.leg = FALSE)
expect_identical(ucl(x), ucl(pmsn_ties))
x <- plot_poppr_msn(gend, pmsn_ties, pop.leg = FALSE, size.leg = TRUE, scale.leg = FALSE)
expect_identical(ucl(x), ucl(pmsn_ties))
x <- plot_poppr_msn(gend, pmsn_ties, pop.leg = TRUE, size.leg = TRUE, scale.leg = FALSE)
expect_identical(ucl(x), ucl(pmsn_ties))
x <- plot_poppr_msn(gend, pmsn_ties, pop.leg = FALSE, size.leg = FALSE, scale.leg = TRUE)
expect_identical(ucl(x), ucl(pmsn_ties))
x <- plot_poppr_msn(gend, pmsn_ties, pop.leg = TRUE, size.leg = FALSE, scale.leg = TRUE)
expect_identical(ucl(x), ucl(pmsn_ties))
x <- plot_poppr_msn(gend, pmsn_ties, pop.leg = FALSE, size.leg = TRUE, scale.leg = TRUE)
expect_identical(ucl(x), ucl(pmsn_ties))
x <- plot_poppr_msn(gend, pmsn_ties, pop.leg = TRUE, size.leg = TRUE, scale.leg = TRUE)
expect_identical(ucl(x), ucl(pmsn_ties))
})
test_that("plot_poppr_msn throws a warning if the user tries nodebase", {
skip_on_cran()
expect_warning(plot_poppr_msn(gend, pmsn_ties, nodebase = 1.15),
"Please use.+nodescale")
expect_warning(plot_poppr_msn(gend, pmsn_ties, nodebase = 1),
"reverting to nodebase = 1.15")
})
test_that("edges can be deleted", {
skip_on_cran()
graph_to_trim <- pmsn_ties
graph_to_trim$graph <- igraph::set_edge_attr(pmsn_ties$graph, "weight", 4, 0.5)
x <- plot_poppr_msn(gend, graph_to_trim, cutoff = 0.25)
expect_ecount(graph_to_trim, 4L)
expect_ecount(x, 3L)
# warning if the cutoff is too low
expect_warning(plot_poppr_msn(gend, pmsn_ties, cutoff = 0.01),
"Cutoff value \\(0.01\\) is below the minimum observed")
})
context("MSN and collapsed MLG tests")
gmsnt <- bruvo.msn(gend, replen = c(1, 1), threshold = 0.15)
test_that("Minimum spanning networks also collapse MLGs", {
skip_on_cran()
gend <- as.genclone(gend)
gend_single <- as.genclone(gend_single)
# Adding the filter for testing
mlg.filter(gend, dist = bruvo.dist, replen = c(1, 1)) <- 0.15
mll(gend) <- "original"
expect_vcount(gmsnt, 2)
pgmsnt <- poppr.msn(gend, distmat = gend_bruvo, threshold = 0.15)
mll(gend) <- "contracted"
gmsnot <- bruvo.msn(gend, replen = c(1, 1)) # no threshold supplied
gmsnone <- bruvo.msn(gend, replen = c(1, 1), threshold = 0.3)
expect_vcount(gmsnone, 1)
gmsnall <- bruvo.msn(gend, replen = c(1, 1), threshold = 0)
expect_vcount(gmsnall, 4)
expect_identical_vertex_attr(gmsnt, pgmsnt, "pie")
expect_identical_vertex_attr(gmsnot, pgmsnt, "pie")
expect_identical_vertex_attr(gmsnt, pgmsnt, "name")
expect_identical_vertex_attr(gmsnot, pgmsnt, "name")
expect_identical_edge_attr(gmsnt, pgmsnt, "weight")
expect_identical_edge_attr(gmsnot, pgmsnt, "weight")
mll(gend) <- "original"
gmsn <- bruvo.msn(gend, replen = c(1, 1), showplot = FALSE)
expect_vcount(gmsn, 4)
pgmsn <- poppr.msn(gend, distmat = gend_bruvo, showplot = FALSE)
expect_identical_vertex_attr(gmsn, pgmsn, "pie")
expect_identical_vertex_attr(gmsn, gmsnall, "pie")
expect_identical_vertex_attr(gmsn, pgmsn, "name")
expect_identical_vertex_attr(gmsn, gmsnall, "name")
expect_identical_edge_attr(gmsn, pgmsn, "weight")
expect_identical_edge_attr(gmsn, gmsnall, "weight")
})
test_that("Minimum spanning networks can collapse MLGs with single populations", {
skip_on_cran()
sgmsnt <- bruvo.msn(gend_single, replen = c(1, 1), threshold = 0.15)
psgmsnt <- poppr.msn(gend_single, distmat = gend_bruvo, threshold = 0.15)
expect_identical_vertex_attr(sgmsnt, psgmsnt, "pie")
expect_identical_vertex_attr(sgmsnt, psgmsnt, "name")
expect_identical_edge_attr(sgmsnt, psgmsnt, "weight")
sgmsn <- bruvo.msn(gend_single, replen = c(1, 1), showplot = FALSE)
psgmsn <- poppr.msn(gend_single, distmat = gend_bruvo, showplot = FALSE)
expect_identical_vertex_attr(sgmsn, psgmsn, "pie")
expect_identical_vertex_attr(sgmsn, psgmsn, "name")
expect_identical_edge_attr(sgmsn, psgmsn, "weight")
expect_vcount(sgmsnt, 2)
expect_vcount(sgmsn, 4)
expect_output(plot_poppr_msn(gend, gmsnt, palette = "cm.colors"), NA)
expect_output(plot_poppr_msn(gend_single, sgmsnt, palette = "cm.colors"), NA)
})
test_that("Filtered minimum spanning networks retain original names", {
skip_on_cran()
# setup ----------------------------------------------------
grid_example <- matrix(c(1, 4,
1, 1,
5, 1,
9, 1,
9, 4),
ncol = 2,
byrow = TRUE)
rownames(grid_example) <- LETTERS[1:5]
colnames(grid_example) <- c("x", "y")
grid_new <- rbind(grid_example,
new = c(5, NA),
mut = c(5, 2)
)
x <- as.genclone(df2genind(grid_new, ploidy = 1))
indNames(x)
## [1] "A" "B" "C" "D" "E" "new" "mut"
raw_dist <- function(x){
dist(genind2df(x, usepop = FALSE))
}
(xdis <- raw_dist(x))
# normal ---------------------------------------------------
set.seed(9001)
g1 <- poppr.msn(x, xdis, include.ties = TRUE,
vertex.label.color = "firebrick", vertex.label.font = 2)
all_names <- igraph::V(g1$graph)$name
## [1] "A" "B" "C" "D" "E" "new" "mut"
# filtered ---------------------------------------------------
set.seed(9001)
g1.1 <- poppr.msn(x, xdis, threshold = 1, include.ties = TRUE,
vertex.label.color = "firebrick", vertex.label.font = 2)
cc_names <- igraph::V(g1.1$graph)$name
## [1] "A" "B" "C" "D" "E" "new"
expect_identical(cc_names, head(all_names, -1))
})
context("minimum spanning network subset populations")
data("partial_clone")
pc <- as.genclone(partial_clone)
bpc <- bruvo.dist(pc, replen = rep(1, 10))
bmsn <- bruvo.msn(pc, replen = rep(1, 10), showplot = FALSE)
pmsn <- poppr.msn(pc, bpc, showplot = FALSE)
test_that("nodes are properly scaled", {
expect_vertex_size_scale(bmsn, as.integer(table(mll(pc))))
expect_vertex_size_scale(pmsn, as.integer(table(mll(pc))))
})
test_that("a warning is thrown if there are no populations to subset", {
skip_on_cran()
pc2 <- pc
pop(pc2) <- NULL
expect_warning(poppr.msn(pc2, dist(pc), showplot = FALSE, sublist = 1),
"Subsetting not taking place")
expect_warning(bruvo.msn(pc2, replen = rep(1, 10), showplot = FALSE, sublist = 1),
"Subsetting not taking place")
})
test_that("Minimum spanning networks can subset populations", {
expect_identical(ucl(bmsn), ucl(pmsn))
bmsn12 <- bruvo.msn(pc, replen = rep(1, 10), sublist = 1:2, showplot = FALSE)
pmsn12 <- poppr.msn(pc, bpc, sublist = 1:2, showplot = FALSE)
expect_identical(ucl(bmsn12), ucl(pmsn12))
bmsn1 <- bruvo.msn(pc, replen = rep(1, 10), sublist = 1, showplot = FALSE)
pmsn1 <- poppr.msn(pc, bpc, sublist = 1, showplot = FALSE)
expect_identical(ucl(bmsn1), ucl(pmsn1))
})
context("custom MLLs and minimum spanning networks")
mll.custom(pc) <- LETTERS[mll(pc)]
mll.levels(pc)[mll.levels(pc) == "Q"] <- "M"
mll(pc) <- "custom"
test_that("msn works with custom MLLs", {
skip_on_cran()
expect_error(pcmsn <- bruvo.msn(pc, replen = rep(1, 10)), NA)
expect_equivalent(sort(unique(igraph::V(pcmsn$graph)$label)), sort(mll.levels(pc)))
expect_error(plot_poppr_msn(pc, pcmsn), NA)
expect_error(plot_poppr_msn(pc, pcmsn, mlg = TRUE), NA)
})
context("Minimum spanning network aesthetics")
test_that("vectors can be used to color graphs", {
skip_on_cran()
data(Aeut)
A.dist <- diss.dist(Aeut)
# Graph it.
A.msn <- poppr.msn(Aeut, A.dist, gadj=15, vertex.label=NA, showplot = FALSE)
unpal <- c("black", "orange")
fpal <- function(x) unpal
npal <- setNames(unpal, c("Athena", "Mt. Vernon"))
xpal <- c(npal, JoMo = "awesome")
# Using palette without names
uname_pal <- plot_poppr_msn(Aeut, A.msn, palette = unpal)$colors
# Using palette with function
fun_pal <- plot_poppr_msn(Aeut, A.msn, palette = fpal)$colors
# Using palette with names
name_pal <- plot_poppr_msn(Aeut, A.msn, palette = npal[2:1])$colors
# Using palette with extra names
xname_pal <- plot_poppr_msn(Aeut, A.msn, palette = xpal)$colors
expect_identical(uname_pal, npal)
expect_identical(fun_pal, npal)
expect_identical(name_pal, npal)
expect_identical(xname_pal, npal)
})