From 94be54a8a80bd7c0dc2c80a7de6caba0896c9ef3 Mon Sep 17 00:00:00 2001
From: Luke Zappia <luke.zappia@mcri.edu.au>
Date: Thu, 20 Jul 2017 04:13:33 +0000
Subject: [PATCH] Merge branch 'master' into devel
* master:
Change mean-dropout to mean-zeros
Add verbose to scDDEstimate
From: Luke Zappia <lazappi@users.noreply.github.com>
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@131415 bc3139a8-67e5-0310-9ffc-ced21a209358
---
DESCRIPTION | 4 ++--
NEWS.md | 5 +++++
R/compare.R | 4 ++--
R/scDD-estimate.R | 28 +++++++++++++++++++++-------
man/compareSCESets.Rd | 2 +-
man/scDDEstimate.Rd | 8 +++++---
6 files changed, 36 insertions(+), 15 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 594612b..c3b526b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: splatter
Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 1.1.2
-Date: 2017-07-16
+Version: 1.1.3
+Date: 2017-07-20
Author: Luke Zappia
Authors@R:
c(person("Luke", "Zappia", role = c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index 3ced178..36c1579 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,8 @@
+# 1.1.3
+
+* Add verbose option to scDDEstimate
+* Change "mean-dropout" to "mean-zeros" in compareSCESets
+
# 1.1.2
* Update summariseDiff
diff --git a/R/compare.R b/R/compare.R
index ffee65d..45af803 100644
--- a/R/compare.R
+++ b/R/compare.R
@@ -29,7 +29,7 @@
#' \item{\code{ZerosCell}}{Boxplot of the percentage of each cell
#' that is zero.}
#' \item{\code{MeanZeros}}{Scatter plot with fitted lines showing
-#' the mean-dropout relationship.}
+#' the mean-zeros relationship.}
#' }
#' }
#' }
@@ -164,7 +164,7 @@ compareSCESets <- function(sces, point.size = 0.1, point.alpha = 0.1,
scale_fill_manual(values = colours) +
xlab("Mean count") +
ylab("Percentage zeros") +
- ggtitle("Mean-dropout relationship") +
+ ggtitle("Mean-zeros relationship") +
theme_minimal()
if (fits) {
diff --git a/R/scDD-estimate.R b/R/scDD-estimate.R
index 542d3af..f1aba9c 100644
--- a/R/scDD-estimate.R
+++ b/R/scDD-estimate.R
@@ -7,6 +7,7 @@
#' @param conditions Vector giving the condition that each cell belongs to.
#' Conditions can be 1 or 2.
#' @param params SCDDParams object to store estimated values in.
+#' @param verbose logical. Whether to show progress messages.
#' @param BPPARAM A \code{\link[BiocParallel]{BiocParallelParam}} instance
#' giving the parallel back-end to be used. Default is
#' \code{\link[BiocParallel]{SerialParam}} which uses a single core.
@@ -29,23 +30,23 @@
#' @importFrom BiocParallel SerialParam
#' @export
scDDEstimate <- function(counts, conditions, params = newSCDDParams(),
- BPPARAM = SerialParam()) {
+ verbose = TRUE, BPPARAM = SerialParam()) {
UseMethod("scDDEstimate")
}
#' @rdname scDDEstimate
#' @export
scDDEstimate.SCESet <- function(counts, conditions, params = newSCDDParams(),
- BPPARAM = SerialParam()) {
+ verbose = TRUE, BPPARAM = SerialParam()) {
counts <- scater::counts(counts)
- scDDEstimate(counts, conditions, params)
+ scDDEstimate(counts, conditions, params, verbose, BPPARAM)
}
#' @rdname scDDEstimate
#' @importFrom methods as
#' @export
scDDEstimate.matrix <- function(counts, conditions, params = newSCDDParams(),
- BPPARAM = SerialParam()) {
+ verbose = TRUE, BPPARAM = SerialParam()) {
if (!requireNamespace("scDD", quietly = TRUE)) {
stop("The scDD simulation requires the 'scDD' package.")
@@ -61,8 +62,15 @@ scDDEstimate.matrix <- function(counts, conditions, params = newSCDDParams(),
counts.list <- list(Cond1 = counts[, conditions == 1],
Cond2 = counts[, conditions == 2])
- processed <- scDD::preprocess(counts.list, c("Cond1", "Cond2"),
- median_norm = TRUE)
+ if (verbose) {
+ processed <- scDD::preprocess(counts.list, c("Cond1", "Cond2"),
+ median_norm = TRUE)
+ } else {
+ suppressMessages(
+ processed <- scDD::preprocess(counts.list, c("Cond1", "Cond2"),
+ median_norm = TRUE)
+ )
+ }
assays <- S4Vectors::SimpleList(NormCounts = processed)
@@ -72,7 +80,13 @@ scDDEstimate.matrix <- function(counts, conditions, params = newSCDDParams(),
SCdat <- SummarizedExperiment::SummarizedExperiment(assays = assays,
colData = colData)
- SCdat <- scDD::scDD(SCdat, testZeroes = FALSE, param = BPPARAM)
+ if (verbose) {
+ SCdat <- scDD::scDD(SCdat, testZeroes = FALSE, param = BPPARAM)
+ } else {
+ dummy <- utils::capture.output(suppressMessages(
+ SCdat <- scDD::scDD(SCdat, testZeroes = FALSE, param = BPPARAM)
+ ))
+ }
res <- scDD::results(SCdat)
res <- res[!is.na(res$DDcategory), ]
diff --git a/man/compareSCESets.Rd b/man/compareSCESets.Rd
index 126acbc..4c4393c 100644
--- a/man/compareSCESets.Rd
+++ b/man/compareSCESets.Rd
@@ -45,7 +45,7 @@ The returned list has three items:
\item{\code{ZerosCell}}{Boxplot of the percentage of each cell
that is zero.}
\item{\code{MeanZeros}}{Scatter plot with fitted lines showing
- the mean-dropout relationship.}
+ the mean-zeros relationship.}
}
}
}
diff --git a/man/scDDEstimate.Rd b/man/scDDEstimate.Rd
index 259a698..44bd401 100644
--- a/man/scDDEstimate.Rd
+++ b/man/scDDEstimate.Rd
@@ -6,14 +6,14 @@
\alias{scDDEstimate.matrix}
\title{Estimate scDD simulation parameters}
\usage{
-scDDEstimate(counts, conditions, params = newSCDDParams(),
+scDDEstimate(counts, conditions, params = newSCDDParams(), verbose = TRUE,
BPPARAM = SerialParam())
\method{scDDEstimate}{SCESet}(counts, conditions, params = newSCDDParams(),
- BPPARAM = SerialParam())
+ verbose = TRUE, BPPARAM = SerialParam())
\method{scDDEstimate}{matrix}(counts, conditions, params = newSCDDParams(),
- BPPARAM = SerialParam())
+ verbose = TRUE, BPPARAM = SerialParam())
}
\arguments{
\item{counts}{either a counts matrix or an SCESet object containing count
@@ -24,6 +24,8 @@ Conditions can be 1 or 2.}
\item{params}{SCDDParams object to store estimated values in.}
+\item{verbose}{logical. Whether to show progress messages.}
+
\item{BPPARAM}{A \code{\link[BiocParallel]{BiocParallelParam}} instance
giving the parallel back-end to be used. Default is
\code{\link[BiocParallel]{SerialParam}} which uses a single core.}
--
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