Rename path.length to path.nSteps

R/AllClasses.R

@@ -167,9 +167,10 @@ setClass("SimpleParams",
 #'             this form would have a "from" parameter of c(0, 1, 1) (where 0 is
 #'             the origin). If no vector is given all paths will start at the
 #'             origin.}
-#'             \item{\code{[path.length]}}{Vector giving the number of steps to
+#'             \item{\code{[path.nSteps]}}{Vector giving the number of steps to
 #'             simulate along each path. If a single value is given it will be
-#'             applied to all paths.}
+#'             applied to all paths. This parameter was previously called
+#'             \code{path.length}.}
 #'             \item{\code{[path.skew]}}{Vector giving the skew of each path.
 #'             Values closer to 1 will give more cells towards the starting
 #'             population, values closer to 0 will give more cells towards the
@@ -221,7 +222,7 @@ setClass("SplatParams",
                    dropout.mid = "numeric",
                    dropout.shape = "numeric",
                    path.from = "numeric",
-                   path.length = "numeric",
+                   path.nSteps = "numeric",
                    path.skew = "numeric",
                    path.nonlinearProb = "numeric",
                    path.sigmaFac = "numeric"),
@@ -249,7 +250,7 @@ setClass("SplatParams",
                                dropout.mid = 0,
                                dropout.shape = -1,
                                path.from = 0,
-                               path.length = 100,
+                               path.nSteps = 100,
                                path.skew = 0.5,
                                path.nonlinearProb = 0.1,
                                path.sigmaFac = 0.8))

R/SplatParams-methods.R

@@ -54,8 +54,8 @@ setValidity("SplatParams", function(object) {
                                              any.missing = FALSE, min.len = 1),
                 path.from = checkIntegerish(v$path.from, lower = 0,
                                             upper = nGroups, len = nGroups),
-                path.length = checkIntegerish(v$path.length, lower = 1,
-                                               len = nGroups),
+                path.nSteps = checkIntegerish(v$path.nSteps, lower = 1,
+                                              len = nGroups),
                 path.skew = checkNumeric(v$path.skew, lower = 0, upper = 1,
                                          len = nGroups),
                 path.nonlinearProb = checkNumber(v$path.nonlinearProb,
@@ -103,6 +103,12 @@ setValidity("SplatParams", function(object) {
 setMethod("setParam", "SplatParams", function(object, name, value) {
     checkmate::assertString(name)
 
+    if (name == "path.length") {
+        warning("path.length has been renamed path.nSteps, ",
+                "please use path.nSteps in the future.")
+        name <- "path.nSteps"
+    }
+
     if (name == "nCells" || name == "nBatches") {
         stop(name, " cannot be set directly, set batchCells instead")
     }
@@ -211,7 +217,7 @@ setMethod("show", "SplatParams", function(object) {
                                      "(Midpoint)"     = "dropout.mid",
                                      "(Shape)"        = "dropout.shape"),
                "Paths:"          = c("[From]"         = "path.from",
-                                     "[Length]"       = "path.length",
+                                     "[Steps]"        = "path.nSteps",
                                      "[Skew]"         = "path.skew",
                                      "[Non-linear]"   = "path.nonlinearProb",
                                      "[Sigma Factor]" = "path.sigmaFac"))
@@ -232,7 +238,7 @@ setMethod("expandParams", "SplatParams", function(object) {
     n <- getParam(object, "nGroups")
 
     vectors <- c("de.prob", "de.downProb", "de.facLoc", "de.facScale",
-                 "path.from", "path.length", "path.skew")
+                 "path.from", "path.nSteps", "path.skew")
 
     object <- callNextMethod(object, vectors, n)
 

R/splat-simulate.R

@@ -530,7 +530,7 @@ splatSimPathCellMeans <- function(sim, params) {
     cell.names <- colData(sim)$Cell
     gene.names <- rowData(sim)$Gene
     path.from <- getParam(params, "path.from")
-    path.length <- getParam(params, "path.length")
+    path.nSteps <- getParam(params, "path.nSteps")
     path.skew <- getParam(params, "path.skew")
     path.nonlinearProb <- getParam(params, "path.nonlinearProb")
     path.sigmaFac <- getParam(params, "path.sigmaFac")
@@ -558,7 +558,7 @@ splatSimPathCellMeans <- function(sim, params) {
         rowData(sim)[[paste0("SigmaFacPath", idx)]] <- sigma.facs
     }
 
-    # Generate paths. Each path is a matrix with path.length columns and
+    # Generate paths. Each path is a matrix with path.nSteps columns and
     # nGenes rows where the expression from each genes changes along the path.
     path.steps <- lapply(seq_along(path.from), function(idx) {
         from <- path.from[idx]
@@ -575,7 +575,7 @@ splatSimPathCellMeans <- function(sim, params) {
         sigma.facs <- rowData(sim)[[paste0("SigmaFacPath", idx)]]
 
         # Build Brownian bridges from start to end
-        steps <- buildBridges(facs.start, facs.end, n = path.length[idx],
+        steps <- buildBridges(facs.start, facs.end, n = path.nSteps[idx],
                               sigma.fac = sigma.facs)
 
         return(t(steps))
@@ -584,13 +584,13 @@ splatSimPathCellMeans <- function(sim, params) {
     # Randomly assign a position in the appropriate path to each cell
     path.probs <- lapply(seq_len(nGroups), function(idx) {
         probs <- seq(path.skew[idx], 1 - path.skew[idx],
-                          length = path.length[idx])
+                          length = path.nSteps[idx])
         probs <- probs / sum(probs)
         return(probs)
     })
 
     steps <- sapply(factor(groups), function(path) {
-        step <- sample(seq_len(path.length[path]), 1, prob = path.probs[[path]])
+        step <- sample(seq_len(path.nSteps[path]), 1, prob = path.probs[[path]])
     })
 
     # Collect the underlying expression levels for each cell

man/SplatParams.Rd

@@ -111,9 +111,10 @@ The Splatter simulation requires the following parameters:
             this form would have a "from" parameter of c(0, 1, 1) (where 0 is
             the origin). If no vector is given all paths will start at the
             origin.}
-            \item{\code{[path.length]}}{Vector giving the number of steps to
+            \item{\code{[path.nSteps]}}{Vector giving the number of steps to
             simulate along each path. If a single value is given it will be
-            applied to all paths.}
+            applied to all paths. This parameter was previously called
+            \code{path.length}.}
             \item{\code{[path.skew]}}{Vector giving the skew of each path.
             Values closer to 1 will give more cells towards the starting
             population, values closer to 0 will give more cells towards the

vignettes/splatter.Rmd

@@ -137,7 +137,7 @@ The parameters required for the Splat simulation are briefly described here:
     * `dropout.shape` - Shape parameter for the dropout logistic function.
 * **Differentiation path parameters**
     * `path.from` - Vector giving the originating point of each path.
-    * `path.length` - Vector giving the number of steps to simulate along each
+    * `path.steps` - Vector giving the number of steps to simulate along each
       path.
     * `path.skew` - Vector giving the skew of each path.
     * `path.nonlinearProb` - Probability that a gene changes expression in a