v0.1.0

Author: quantixed

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: SuperPlotR
 Title: Making SuperPlots in R
-Version: 0.0.8
+Version: 0.1.0
 Authors@R:
     person(given = "Stephen J",
            family = "Royle",
@@ -16,7 +16,7 @@ Description: SuperPlots are a way to show experimental data in a way that
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Depends: 
     R (>= 2.10)
 Config/rcmdcheck/ignore-inconsequential-notes: true
@@ -31,5 +31,7 @@ URL: https://github.com/quantixed/SuperPlotR, https://quantixed.github.io/SuperP
 BugReports: https://github.com/quantixed/SuperPlotR/issues
 Suggests: 
     knitr,
-    rmarkdown
+    rmarkdown,
+    testthat (>= 3.0.0)
 VignetteBuilder: knitr
+Config/testthat/edition: 3

NEWS.md

@@ -1,4 +1,8 @@
-# SuperPlotR (development version)
+# SuperPlotR
+
+## SuperPlotR 0.1.0
+
+* Test structure added. Bumping to 0.1.0 to reflect this change.
 
 ## SuperPlotR 0.0.8
 

tests/testthat.R

@@ -0,0 +1,16 @@
+library(testthat)
+library(SuperPlotR)
+
+test_check("SuperPlotR")
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(SuperPlotR)
+
+test_check("SuperPlotR")

tests/testthat/test-add-sp-bars.R

@@ -0,0 +1,10 @@
+test_that("add_sp_bars adds errorbar and crossbar layers", {
+  df <- data.frame(group = rep(c("A","B"), each = 5),
+                   value = c(rep(1,5), rep(2,5)),
+                   repl = rep(1:5, 2))
+  p0 <- ggplot2::ggplot(df, ggplot2::aes(x = group, y = value))
+  p <- add_sp_bars(p0, bars = "mean_sem", df = df, cond = "group", rep_summary = "value")
+  expect_s3_class(p, "ggplot")
+  layer_classes <- vapply(p$layers, function(l) class(l$geom)[1], character(1))
+  expect_true(any(grepl("GeomErrorbar|GeomCrossbar", layer_classes)))
+})

tests/testthat/test-get-sp-colours.R

@@ -0,0 +1,15 @@
+test_that("get_sp_colours returns correct length and repeats custom vector", {
+  cols <- get_sp_colours(3, "tol_bright")
+  expect_type(cols, "character")
+  expect_length(cols, 3)
+
+  # custom vector of colours is repeated to length n
+  custom <- c("#FF0000", "green")
+  cols2 <- get_sp_colours(5, custom)
+  expect_length(cols2, 5)
+  expect_equal(cols2[1:2], custom)
+})
+
+test_that("get_sp_colours errors on invalid scheme", {
+  expect_error(get_sp_colours(2, "not_a_palette"))
+})

tests/testthat/test-get-sp-stats.R

@@ -0,0 +1,16 @@
+test_that("get_sp_stats prints sensible messages for edge cases and tests", {
+  df1 <- data.frame(condition = rep("A", 3), rep_mean = c(1,2,3))
+  expect_output(get_sp_stats(df1, "rep_mean", "condition", NULL, 1, 1, "para_unpaired"),
+                "Only one condition")
+
+  df2 <- data.frame(condition = rep(c("X","Y"), each = 2), rep_mean = c(1,2,3,4))
+  # nrepl < 3 should report less than three replicates
+  expect_output(get_sp_stats(df2, "rep_mean", "condition", NULL, 2, 2, "para_unpaired"),
+                "Less than three replicates")
+
+  # a valid two-group t-test path emits 'Performing t-test'
+  df3 <- data.frame(condition = rep(c("X","Y"), each = 3),
+                    rep_mean = c(1,2,3, 4,5,6))
+  expect_output(get_sp_stats(df3, "rep_mean", "condition", NULL, 2, 3, "para_unpaired"),
+                "Performing t-test")
+})

tests/testthat/test-representative.R

@@ -0,0 +1,16 @@
+test_that("representative returns expected structure and ranks", {
+  df <- data.frame(group = rep("G", 5),
+                   repl = rep(1, 5),
+                   value = c(1,2,3,4,5))
+  res <- representative(df, meas = "value", cond = "group", repl = "repl")
+  expect_true(is.data.frame(res))
+  expect_true("rank" %in% names(res))
+  expect_true(all(res$rank >= 1))
+
+  # test with a label column
+  df2 <- df
+  df2$label <- letters[1:5]
+  res2 <- representative(df2, meas = "value", cond = "group", repl = "repl", label = "label")
+  expect_true(is.data.frame(res2))
+  expect_true("label" %in% names(res2))
+})

tests/testthat/test-superplot-structure.R

@@ -0,0 +1,15 @@
+test_that("superplot returns a ggplot and contains expected data rows", {
+  set.seed(42)
+  df <- data.frame(
+    condition = rep(c("C1", "C2"), each = 4),
+    replicate = rep(1:4, times = 2),
+    value = rnorm(8)
+  )
+  p <- superplot(df, meas = "value", cond = "condition", repl = "replicate")
+  expect_s3_class(p, "ggplot")
+
+  gb <- ggplot2::ggplot_build(p)
+  # ensure at least one layer contains data rows
+  total_rows <- sum(vapply(gb$data, nrow, integer(1)))
+  expect_true(total_rows >= 8)
+})

tests/testthat/test-superplot-vdiffr.R

@@ -0,0 +1,6 @@
+test_that("vdiffr visual test for a small superplot (skipped if vdiffr missing)", {
+  testthat::skip_if_not_installed("vdiffr")
+  data(lord_jcb, package = "SuperPlotR")
+  p <- superplot(lord_jcb, meas = "Speed", cond = "Treatment", repl = "Replicate")
+  vdiffr::expect_doppelganger("superplot-lord_jcb", p)
+})