From 9d1a0c9abc7141bd6c60f22d172ad223c5e9a3e6 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Tue, 7 Mar 2017 14:24:12 +1100
Subject: [PATCH] Version 0.99.10
---
DESCRIPTION | 4 ++--
NEWS.md | 7 +++++++
R/compare.R | 19 ++++++++++++++++---
man/compareSCESets.Rd | 2 ++
4 files changed, 27 insertions(+), 5 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 530d696..3ef758f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: splatter
Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 0.99.9
-Date: 2017-02-02
+Version: 0.99.10
+Date: 2017-03-07
Author: Luke Zappia
Authors@R:
c(person("Luke", "Zappia", role = c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index 43207e0..9480f91 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,10 @@
+# 0.99.10
+
+* Improve Splat estimation procedure
+* Update default Splat parameters
+* Remove out.loProb Splat parameter
+* Add MeanZeros plot to compareSCESets
+
# 0.99.9
* Add addGeneLengths function
diff --git a/R/compare.R b/R/compare.R
index 82f2658..989417a 100644
--- a/R/compare.R
+++ b/R/compare.R
@@ -24,6 +24,8 @@
#' that is zero.}
#' \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.}
#' }
#' }
#' }
@@ -95,8 +97,8 @@ compareSCESets <- function(sces) {
mean.var <- ggplot(fData.all,
aes_string(x = "mean_log_cpm", y = "var_log_cpm",
- olour = "Dataset", fill = "Dataset")) +
- geom_point() +
+ colour = "Dataset", fill = "Dataset")) +
+ geom_point(alpha = 0.2) +
geom_smooth() +
xlab(expression(paste("Mean ", log[2], "(CPM + 1)"))) +
ylab(expression(paste("Variance ", log[2], "(CPM + 1)"))) +
@@ -130,6 +132,16 @@ compareSCESets <- function(sces) {
ggtitle("Distribution of zeros per cell") +
theme_minimal()
+ mean.zeros <- ggplot(fData.all,
+ aes_string(x = "mean_log_cpm", y = "pct_dropout",
+ colour = "Dataset", fill = "Dataset")) +
+ geom_point(alpha = 0.2) +
+ geom_smooth() +
+ xlab(expression(paste("Mean ", log[2], "(CPM + 1)"))) +
+ ylab(expression(paste("Percentage zeros"))) +
+ ggtitle("Mean-dropout relationship") +
+ theme_minimal()
+
comparison <- list(FeatureData = fData.all,
PhenoData = pData.all,
Plots = list(Means = means,
@@ -137,7 +149,8 @@ compareSCESets <- function(sces) {
MeanVar = mean.var,
LibrarySizes = libs,
ZerosGene = z.gene,
- ZerosCell = z.cell))
+ ZerosCell = z.cell,
+ MeanZeros = mean.zeros))
return(comparison)
}
diff --git a/man/compareSCESets.Rd b/man/compareSCESets.Rd
index b66c525..14eb59d 100644
--- a/man/compareSCESets.Rd
+++ b/man/compareSCESets.Rd
@@ -35,6 +35,8 @@ The return list has three items:
that is zero.}
\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.}
}
}
}
--
GitLab