diff --git a/DESCRIPTION b/DESCRIPTION index 530d696732d9a2b63f192c508f7407d239ff03b6..3ef758f6696565391eb13544142c7a0b347c100f 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 43207e0429ec2c06975707360281973d7eab0fd5..9480f9171c1184640bb042a31ba60ee3454e50c6 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 82f26583831f18b85b18a5b3076be6d410d06f0b..989417a0b263d5d3f145ab995e32f25b0f7c6cac 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 b66c525475e8d11a35569dee1615c2226f1d8caa..14eb59dca842ebf7e10f78a612da9155b6b73a8c 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.} } } }