Run checks

R/compare.R

@@ -42,7 +42,7 @@
 #'
 #' @return List containing the combined datasets and plots.
 #' @examples
-#' sim1 <- splatSimulate(nGenes = 1000, groupCells = 20)
+#' sim1 <- splatSimulate(nGenes = 1000, batchCells = 20)
 #' sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
 #' comparison <- compareSCESets(list(Splat = sim1, Simple = sim2))
 #' names(comparison)
@@ -249,7 +249,7 @@ compareSCESets <- function(sces, point.size = 0.1, point.alpha = 0.1,
 #'
 #' @return List containing the combined datasets and plots.
 #' @examples
-#' sim1 <- splatSimulate(nGenes = 1000, groupCells = 20)
+#' sim1 <- splatSimulate(nGenes = 1000, batchCells = 20)
 #' sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
 #' difference <- diffSCESets(list(Splat = sim1, Simple = sim2), ref = "Simple")
 #' names(difference)
@@ -521,7 +521,7 @@ diffSCESets <- function(sces, ref, point.size = 0.1, point.alpha = 0.1,
 #'
 #' @examples
 #' \dontrun{
-#' sim1 <- splatSimulate(nGenes = 1000, groupCells = 20)
+#' sim1 <- splatSimulate(nGenes = 1000, batchCells = 20)
 #' sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
 #' comparison <- compareSCESets(list(Splat = sim1, Simple = sim2))
 #' panel <- makeCompPanel(comparison)
@@ -605,7 +605,7 @@ makeCompPanel <- function(comp, title = "Comparison",
 #'
 #' @examples
 #' \dontrun{
-#' sim1 <- splatSimulate(nGenes = 1000, groupCells = 20)
+#' sim1 <- splatSimulate(nGenes = 1000, batchCells = 20)
 #' sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
 #' difference <- diffSCESets(list(Splat = sim1, Simple = sim2), ref = "Simple")
 #' panel <- makeDiffPanel(difference)
@@ -697,7 +697,7 @@ makeDiffPanel <- function(diff, title = "Difference comparison",
 #'
 #' @examples
 #' \dontrun{
-#' sim1 <- splatSimulate(nGenes = 1000, groupCells = 20)
+#' sim1 <- splatSimulate(nGenes = 1000, batchCells = 20)
 #' sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
 #' comparison <- compSCESets(list(Splat = sim1, Simple = sim2))
 #' difference <- diffSCESets(list(Splat = sim1, Simple = sim2), ref = "Simple")
@@ -798,7 +798,7 @@ makeOverallPanel <- function(comp, diff, title = "Overall comparison",
 #'
 #' @return List with MADs, ranks and both combined in long format
 #' @examples
-#' sim1 <- splatSimulate(nGenes = 1000, groupCells = 20)
+#' sim1 <- splatSimulate(nGenes = 1000, batchCells = 20)
 #' sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
 #' difference <- diffSCESets(list(Splat = sim1, Simple = sim2), ref = "Simple")
 #' summary <- summariseDiff(difference)

man/compareSCESets.Rd

@@ -57,7 +57,7 @@ and should be in the correct format to allow you to create further plots
 using \code{\link[ggplot2]{ggplot}}.
 }
 \examples{
-sim1 <- splatSimulate(nGenes = 1000, groupCells = 20)
+sim1 <- splatSimulate(nGenes = 1000, batchCells = 20)
 sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
 comparison <- compareSCESets(list(Splat = sim1, Simple = sim2))
 names(comparison)

man/diffSCESets.Rd

@@ -77,7 +77,7 @@ and should be in the correct format to allow you to create further plots
 using \code{\link[ggplot2]{ggplot}}.
 }
 \examples{
-sim1 <- splatSimulate(nGenes = 1000, groupCells = 20)
+sim1 <- splatSimulate(nGenes = 1000, batchCells = 20)
 sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
 difference <- diffSCESets(list(Splat = sim1, Simple = sim2), ref = "Simple")
 names(difference)

man/makeCompPanel.Rd

@@ -23,7 +23,7 @@ Combine the plots from \code{compareSCESets} into a single panel.
 }
 \examples{
 \dontrun{
-sim1 <- splatSimulate(nGenes = 1000, groupCells = 20)
+sim1 <- splatSimulate(nGenes = 1000, batchCells = 20)
 sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
 comparison <- compareSCESets(list(Splat = sim1, Simple = sim2))
 panel <- makeCompPanel(comparison)

man/makeDiffPanel.Rd

@@ -23,7 +23,7 @@ Combine the plots from \code{diffSCESets} into a single panel.
 }
 \examples{
 \dontrun{
-sim1 <- splatSimulate(nGenes = 1000, groupCells = 20)
+sim1 <- splatSimulate(nGenes = 1000, batchCells = 20)
 sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
 difference <- diffSCESets(list(Splat = sim1, Simple = sim2), ref = "Simple")
 panel <- makeDiffPanel(difference)

man/makeOverallPanel.Rd

@@ -27,7 +27,7 @@ single panel.
 }
 \examples{
 \dontrun{
-sim1 <- splatSimulate(nGenes = 1000, groupCells = 20)
+sim1 <- splatSimulate(nGenes = 1000, batchCells = 20)
 sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
 comparison <- compSCESets(list(Splat = sim1, Simple = sim2))
 difference <- diffSCESets(list(Splat = sim1, Simple = sim2), ref = "Simple")

man/summariseDiff.Rd

@@ -18,7 +18,7 @@ properties are sorted, differences calculated, the Median Absolute Deviation
 taken as the summary statistic and the ranks calculated.
 }
 \examples{
-sim1 <- splatSimulate(nGenes = 1000, groupCells = 20)
+sim1 <- splatSimulate(nGenes = 1000, batchCells = 20)
 sim2 <- simpleSimulate(nGenes = 1000, nCells = 20)
 difference <- diffSCESets(list(Splat = sim1, Simple = sim2), ref = "Simple")
 summary <- summariseDiff(difference)

tests/testthat/test-SplatParams.R

@@ -21,7 +21,7 @@ test_that("path.from checks work", {
     expect_silent(validObject(params))
     params <- setParamUnchecked(params, "path.from", c(0, 3))
     expect_error(validObject(params),
-                 paste('invalid class “SplatParams” object: path.from:',
+                 paste('invalid class "SplatParams" object: path.from:',
                        "All elements must be <= 2"))
     params <- setParamUnchecked(params, "path.from", c(1, 0))
     expect_error(validObject(params), "path cannot begin at itself")

tests/testthat/test-splat-simulate.R

 context("Splatter simulations")
 
-test.params <- newSplatParams(nGenes = 100, groupCells = c(5, 5), lib.scale = 0)
+test.params <- newSplatParams(nGenes = 100, batchCells = c(5, 5),
+                              group.prob = c(0.5, 0.5), lib.scale = 0)
 
 test_that("splatSimulate output is valid", {
     expect_true(validObject(splatSimulate(test.params, method = "single")))
@@ -10,10 +11,10 @@ test_that("splatSimulate output is valid", {
 
 test_that("one group switches to single mode", {
     expect_warning(splatSimulate(test.params, method = "groups",
-                                 groupCells = c(10)),
+                                 group.prob = c(1)),
                    "nGroups is 1, switching to single mode")
     expect_silent(splatSimulate(test.params, method = "paths",
-                                groupCells = c(10), verbose = FALSE))
+                                group.prob = c(1), verbose = FALSE))
 })
 
 test_that("infinite bcv.df is detected", {