Merge pull request #67 from PF2-pasteur-fr/development

1.6.8
PF2-pasteur-fr · May 29, 2019 · f8ba2d9 · f8ba2d9
2 parents e5db42a + 7012177
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: SARTools
 Type: Package
 Title: Statistical Analysis of RNA-Seq Tools
-Version: 1.6.7
-Date: 2019-05-07
+Version: 1.6.8
+Date: 2019-05-29
 Author: Marie-Agnes Dillies and Hugo Varet
 Maintainer: Hugo Varet <[email protected]>
 Depends: R (>= 3.3.0), DESeq2 (>= 1.12.0), edgeR (>= 3.12.0), xtable

diff --git a/NEWS b/NEWS
@@ -1,3 +1,8 @@
+CHANGES IN VERSION 1.6.8
+------------------------
+	o fixed a bug to build the vignette when installing the package from GitHub
+	o new size for the sample names in pairwiseScatterPlots()
+
 CHANGES IN VERSION 1.6.7
 ------------------------
         o modified the installation guidelines for the Bioconductor packages

diff --git a/R/pairwiseScatterPlots.R b/R/pairwiseScatterPlots.R
@@ -17,12 +17,12 @@ pairwiseScatterPlots <- function(counts, group, outfile=TRUE){
     lower.panel <- function(x,y,...){
       horizontal <- (par("usr")[1] + par("usr")[2]) / 2;
       vertical <- (par("usr")[3] + par("usr")[4]) / 2; 
-      text(horizontal, vertical, round(SERE(2^cbind(x,y) - 1), digits=2), cex=ncol/2.5)
+      text(horizontal, vertical, round(SERE(2^cbind(x,y) - 1), digits=2), cex=sqrt(ncol))
     }
     # use of the paris function
     pairs(log2(counts+1), panel=panel, lower.panel=lower.panel,
-          las=1, labels=paste(colnames(counts),group,sep="\n"),
-          main="Pairwise scatter plot",cex.labels=ncol/2,cex.main=ncol/4)
+          las=1, labels=paste(colnames(counts), group, sep="\n"),
+          main="Pairwise scatter plot", cex.labels=sqrt(ncol), cex.main=ncol/4)
     if (outfile) dev.off()
   } else{
     warning("No pairwise scatter-plot produced because of a too high number of samples (>30).")

diff --git a/README.md b/README.md
@@ -22,13 +22,13 @@ To install the SARTools package from GitHub, open a R session and:
 
 - for Windows users only, install [Rtools](https://cran.r-project.org/bin/windows/Rtools/) or check that it is already installed (needed to build the package)
 - load the devtools R package with `library(devtools)`
-- run `install_github("PF2-pasteur-fr/SARTools", build_vignettes=TRUE)`
+- run `install_github("PF2-pasteur-fr/SARTools", build_opts="--no-resave-data")`
 
 ### Using Conda
 
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/r-sartools/README.html)
 
-1. Install [miniconda2](http://conda.pydata.org/miniconda.html)
+1. Install [miniconda](https://docs.conda.io/en/latest/miniconda.html)
 2. Install the SARTools R library and its dependencies using conda `conda install r-sartools`
 
 Note: if you want to set a dedicated conda environment for SARTools, use `conda create -n sartools r-sartools` and follow the instructions to activate it.