Add seed paramater and seed simulation

DESCRIPTION

 Package: splatter
 Type: Package
 Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 0.3.18
+Version: 0.3.19
 Date: 2016-10-11
 Author: Luke Zappia
 Authors@R: as.person(c(

R/params.R

@@ -83,6 +83,7 @@
 #'             value will result in more extreme non-linear variations along a
 #'             path.
 #'   }
+#'   \item seed - Random seed used during the simulation
 #' }
 #'
 #' Those shown in brackets cannot currently be easily estimated from a real
@@ -105,7 +106,8 @@ splatParams <- function(...) {
                    bcv = list(common = NA, DF = NA),
                    dropout = list(present = NA, mid = NA, shape = NA),
                    path = list(from = NA, length = NA, skew = NA,
-                               nonlinearProb = NA, sigmaFac = NA))
+                               nonlinearProb = NA, sigmaFac = NA),
+                   seed = NA)
 
     class(params) <- "splatParams"
 
@@ -155,7 +157,8 @@ print.splatParams <- function(x, ...) {
                                          "[Length]"       = "path.length",
                                          "[Skew]"         = "path.skew",
                                          "[Non-linear]"   = "path.nonlinearProb",
-                                         "[Sigma Factor]" = "path.sigmaFac"))
+                                         "[Sigma Factor]" = "path.sigmaFac"),
+               "Seed:"               = c("Seed"           = "seed"))
 
     for (category in names(pp)) {
         parameters <- getParams(x, pp[[category]])
@@ -332,7 +335,7 @@ checkParams <- function(params) {
                dropout.present = "LOG", dropout.mid = "NUM",
                dropout.shape = "NUM", path.from = "INT", path.length = "INT",
                path.skew = "PROB", path.nonlinearProb = "PROB",
-               path.sigmaFac = "POS")
+               path.sigmaFac = "POS", seed = "INT")
 
     # Define which parameters are allowed to be vectors
     vectors <- c("groupCells", "path.from", "path.length", "path.skew")
@@ -462,7 +465,7 @@ defaultParams <- function() {
                         dropout.present = TRUE, dropout.mid = 0,
                         dropout.shape = -1, path.from = 0, path.length = 100,
                         path.skew = 0.5, path.nonlinearProb = 0.1,
-                        path.sigmaFac = 0.8)
+                        path.sigmaFac = 0.8, seed = sample(1:1e6, 1))
 
     return(params)
 }

R/simulate.R

@@ -115,6 +115,10 @@ splat <- function(params = defaultParams(), method = c("groups", "paths"),
     params <- mergeParams(params, defaultParams())
     params <- expandPathParams(params)
 
+    # Set random seed
+    seed <- getParams(params, "seed")
+    set.seed(seed)
+
     # Get the parameters we are going to use
     nCells <- getParams(params, "nCells")
     nGenes <- getParams(params, "nGenes")

man/splatParams.Rd

@@ -94,6 +94,7 @@ parameters. It has the following sections and values:
             value will result in more extreme non-linear variations along a
             path.
   }
+  \item seed - Random seed used during the simulation
 }
 
 Those shown in brackets cannot currently be easily estimated from a real

tests/testthat/test-params.R

@@ -185,4 +185,10 @@ test_that("constructor is valid", {
 
 test_that("defaultParams is valid", {
     expect_silent(checkParams(defaultParams()))
+})
+
+test_that("default seed is random", {
+    params1 <- defaultParams()
+    params2 <- defaultParams()
+    expect_false(getParams(params1, "seed") == getParams(params2, "seed"))
 })
\ No newline at end of file