From 22c49d090e20f510dbe2e77e81d7253b6c9a757e Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Tue, 1 Oct 2019 11:18:39 +1000
Subject: [PATCH] Minor Splotch changes
* Change default cells.design to end of path
* Add experimental warning
* Avoid resetting cells.design
---
DESCRIPTION | 7 ++++---
NEWS.md | 6 ++++++
R/AllClasses.R | 4 ++--
R/SplotchParams-methods.R | 18 ++++++++++++++++--
4 files changed, 28 insertions(+), 7 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 9eaece6..4741a42 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: splatter
Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 1.9.7.9015
-Date: 2019-09-26
+Version: 1.9.7.9016
+Date: 2019-10-01
Author: Luke Zappia
Authors@R:
c(person("Luke", "Zappia", role = c("aut", "cre"),
@@ -42,7 +42,8 @@ Imports:
SummarizedExperiment,
utils,
crayon,
- S4Vectors
+ S4Vectors,
+ rlang
Suggests:
BiocStyle,
covr,
diff --git a/NEWS.md b/NEWS.md
index 3cb698f..43dd6ea 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,9 @@
+### Version 1.9.7.9016 (2019-10-01)
+
+* Change the default SplotchParams cell design to place cells at end of path
+* Add one time warning for Splotch simulation
+* Avoid unnecessarily resetting cells.design in SplotchParams
+
### Version 1.9.7.9015 (2019-09-26)
* Add doublets to SplotchSimulate
diff --git a/R/AllClasses.R b/R/AllClasses.R
index 11c05ca..d53646c 100644
--- a/R/AllClasses.R
+++ b/R/AllClasses.R
@@ -410,8 +410,8 @@ setClass("SplotchParams",
cells.design = data.frame(
Path = 1,
Probability = 1,
- Alpha = 0,
- Beta = 1
+ Alpha = 1,
+ Beta = 0
),
doublet.prop = 0,
ambient.scale = 0.05,
diff --git a/R/SplotchParams-methods.R b/R/SplotchParams-methods.R
index c3a51cc..e8bc026 100644
--- a/R/SplotchParams-methods.R
+++ b/R/SplotchParams-methods.R
@@ -11,6 +11,11 @@ newSplotchParams <- function(...) {
stop("The Splotch simulation requires the 'DropletUtils' package.")
}
+ msg <- paste("The Splotch simulation is still experimental and may produce",
+ "unreliable results. Please try it and report any issues to",
+ "https://github.com/Oshlack/splatter/issues.")
+ rlang:::warn_deprecated(msg, id = "warn.splotch")
+
params <- new("SplotchParams")
params <- setParams(params, ...)
@@ -260,11 +265,11 @@ setMethod("setParam", "SplotchParams", function(object, name, value) {
}
if (name == "paths.design" &&
- (nrow(value) != nrow(getParam(object, "paths.design")))) {
+ (nrow(value) != nrow(getParam(object, "cells.design")))) {
warning("cells.design reset to match paths.design")
cells.design <- data.frame(Path = value$Path,
Probability = 1 / nrow(value),
- Alpha = 0, Beta = 1)
+ Alpha = 1, Beta = 0)
object <- setParamUnchecked(object, "cells.design", cells.design)
}
@@ -280,6 +285,15 @@ setMethod("setParams", "SplotchParams", function(object, update = NULL, ...) {
update <- c(update, list(...))
+ # If both cells.design and paths.design are given set cells.design first
+ # to avoid reset warning
+ if ("cells.design" %in% names(update) &&
+ "paths.design" %in% names(update)) {
+ object <- setParamUnchecked(object, "cells.design",
+ update$cells.design)
+ update$cells.design <- NULL
+ }
+
update <- bringItemsForward(update, c("network.graph", "paths.design"))
object <- callNextMethod(object, update)
--
GitLab