diff --git a/R/AllClasses.R b/R/AllClasses.R
index eb6a41484cb206e6fbb9e3c1bda8bc41f6be2133..32f13df826437fc10230d9591df6f8faa580398f 100644
--- a/R/AllClasses.R
+++ b/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))
diff --git a/R/SplatParams-methods.R b/R/SplatParams-methods.R
index 368ca553e73a110f87e952d9624ac76bf64456ba..8a82e79c88b7b991ccd2305b773143f62e4bfa21 100644
--- a/R/SplatParams-methods.R
+++ b/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$path.nonlinearProb,
@@ -103,6 +103,12 @@ setValidity("SplatParams", function(object) {
setMethod("setParam", "SplatParams", function(object, name, value) {
checkmate::assertString(name)
+ if (name == "path.length") {
+ warning("path.length has been renamed path.nSteps, ",
+ "please use path.nSteps in the future.")
+ name <- "path.nSteps"
+ }
+
if (name == "nCells" || name == "nBatches") {
stop(name, " cannot be set directly, set batchCells instead")
}
@@ -211,7 +217,7 @@ setMethod("show", "SplatParams", function(object) {
"(Midpoint)" = "dropout.mid",
"(Shape)" = "dropout.shape"),
"Paths:" = c("[From]" = "path.from",
- "[Length]" = "path.length",
+ "[Steps]" = "path.nSteps",
"[Skew]" = "path.skew",
"[Non-linear]" = "path.nonlinearProb",
"[Sigma Factor]" = "path.sigmaFac"))
@@ -232,7 +238,7 @@ setMethod("expandParams", "SplatParams", function(object) {
n <- getParam(object, "nGroups")
vectors <- c("de.prob", "de.downProb", "de.facLoc", "de.facScale",
- "path.from", "path.length", "path.skew")
+ "path.from", "path.nSteps", "path.skew")
object <- callNextMethod(object, vectors, n)
diff --git a/R/splat-simulate.R b/R/splat-simulate.R
index 0cb90b3246ecbc8c191247a367e9253f878ae7be..efa087fdd0a07116e920b8d2b82cf1a1649b1425 100644
--- a/R/splat-simulate.R
+++ b/R/splat-simulate.R
@@ -530,7 +530,7 @@ splatSimPathCellMeans <- function(sim, params) {
cell.names <- colData(sim)$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
diff --git a/man/SplatParams.Rd b/man/SplatParams.Rd
index 23b089c7d31c3bcad9a80e5dbfc09939134fd24d..bb906f959b313a7dcee5dfd3b5f1d2797f3307a6 100644
--- a/man/SplatParams.Rd
+++ b/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
diff --git a/vignettes/splatter.Rmd b/vignettes/splatter.Rmd
index be82bd389bad6e9e843b646fc9399c7558c133bd..b92584956930bde9ac10e87e101235398fa40a99 100644
--- a/vignettes/splatter.Rmd
+++ b/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