Add extra checks checkParams

Check that path.from has possible values

DESCRIPTION

 Package: splatter
 Type: Package
 Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 0.3.10
+Version: 0.3.11
 Date: 2016-10-10
 Author: Luke Zappia
 Authors@R: as.person(c(

R/params.R

@@ -302,6 +302,8 @@ getParams <- function(params, names) {
 #'   \item{Vector parameters are the correct length}
 #'   \item{Vector parameters do not contain NAs}
 #'   \item{Non-vector parameters are single values}
+#'   \item{nCells, nGroups and groupCells are consistent}
+#'   \item{path.from has possible values}
 #' }
 #'
 #' @return Produces error if not valid otherwise nothing
@@ -321,15 +323,16 @@ checkParams <- function(params) {
     # INT = Positive integer
     # PROB = Positive numeric in range 0-1
     # LOG = Logical
-    types <- c(nGenes = "INT", nCells = "INT", groupCells = "INT",
-               mean.rate = "POS", mean.shape = "POS", lib.loc = "NUM",
-               lib.scale = "POS", out.prob = "PROB", out.loProb = "PROB",
-               out.facLoc = "NUM", out.facScale = "POS", de.prob = "PROB",
-               de.downProb = "PROB", de.facLoc = "NUM", de.facScale = "POS",
-               bcv.common = "POS", bcv.DF = "POS", dropout.present = "LOG",
-               dropout.mid = "NUM", dropout.shape = "NUM", path.from = "INT",
-               path.length = "INT", path.skew = "PROB",
-               path.nonlinearProb = "PROB", path.sigmaFac = "POS")
+    types <- c(nGenes = "INT", nCells = "INT", nGroups = "INT",
+               groupCells = "INT", mean.rate = "POS", mean.shape = "POS",
+               lib.loc = "NUM", lib.scale = "POS", out.prob = "PROB",
+               out.loProb = "PROB", out.facLoc = "NUM", out.facScale = "POS",
+               de.prob = "PROB", de.downProb = "PROB", de.facLoc = "NUM",
+               de.facScale = "POS", bcv.common = "POS", bcv.DF = "POS",
+               dropout.present = "LOG", dropout.mid = "NUM",
+               dropout.shape = "NUM", path.from = "INT", path.length = "INT",
+               path.skew = "PROB", path.nonlinearProb = "PROB",
+               path.sigmaFac = "POS")
 
     # Define which parameters are allowed to be vectors
     vectors <- c("groupCells", "path.from", "path.length", "path.skew")
@@ -385,10 +388,23 @@ checkParams <- function(params) {
     n.cells <- getParams(params, "nCells")
     n.groups <- getParams(params, "nGroups")
     group.cells <- getParams(params, "groupCells")
-    if (!is.na(group.cells) &&
+    if (!all(is.na(group.cells)) &&
         (n.cells != sum(group.cells) || n.groups != length(group.cells))) {
         stop("nCells, nGroups and groupCells are not consistent")
     }
+
+    # Check path.from contains origin, has allowed values and does not reference
+    # itself (no loops)
+    path.from <- getParams(params, "path.from")
+    if (!all(is.na(path.from))) {
+        if (!(0 %in% path.from)) {
+            stop("origin must be specified in path.from")
+        } else if (any(path.from > n.groups)) {
+            stop("values in path.from cannot be greater than number of paths")
+        } else if (any(path.from == 1:n.groups)) {
+            stop("path cannot begin at itself")
+        }
+    }
 }
 
 #' Merge two splatParams objects

man/checkParams.Rd

@@ -27,6 +27,8 @@ The following checks are made:
   \item{Vector parameters are the correct length}
   \item{Vector parameters do not contain NAs}
   \item{Non-vector parameters are single values}
+  \item{nCells, nGroups and groupCells are consistent}
+  \item{path.from has possible values}
 }
 }
 \examples{

tests/testthat/test-params.R

@@ -107,6 +107,22 @@ test_that("checkParams checks groupCells", {
                  "nCells, nGroups and groupCells are not consistent")
 })
 
+test_that("checkParams checks path.from", {
+    params <- splatParams()
+    params <- setParams(params, groupCells = c(10, 10))
+    params$path$from <- c(0, 1)
+    expect_silent(checkParams(params))
+    params$path$from <- c(0, 3)
+    expect_error(checkParams(params),
+                 "values in path.from cannot be greater than number of paths")
+    params$path$from <- c(1, 0)
+    expect_error(checkParams(params), "path cannot begin at itself")
+    params <- splatParams()
+    params <- setParams(params, groupCells = c(10, 10, 10))
+    params$path$from <- c(2, 1, 1)
+    expect_error(checkParams(params), "origin must be specified in path.from")
+})
+
 test_that("setParams sets correctly", {
     params <- splatParams()
     params <- setParams(params, nGenes = 100)