-Added README.md

-Added Tips section to Vignette

Author: dphansti

DESCRIPTION

@@ -2,8 +2,8 @@ Package: Sushi
 Type: Package
 Title: Tools for visualizing genomics data
 Description: Flexible, quantitative, and integrative genomic visualizations for publication-quality multi-panel figures
-Version: 0.99.2
-Date: 2014-02-17
+Version: 1.0.1
+Date: 2014-05-26
 Author: Douglas H Phanstiel <[email protected]>
 Maintainer: Douglas H Phanstiel <[email protected]>
 biocViews: DataRepresentation, Visualization, Genetics, Sequencing, Infrastructure,

README.md

@@ -17,15 +17,17 @@ Detailed usage examples are available in the [Vignette](https://github.com/dphan
 ## Sushi Installation
 
 1. Install with Bioconductor:
-This requires R 3.1 to install
+
+Note: R 3.1 is required for installation via Bioconductor. The newest version of R can be donwloaded at (www.r-project.org/).  Installation via Bioconductor also requires libcurl and libxml2 which may not be be standard with some Linux distributions and are available for download at (http://curl.haxx.se/libcurl/ and http://xmlsoft.org/, respectviely.
+
 ```
 source("http://bioconductor.org/biocLite.R")
 biocLite("Sushi")
 ```
 
-2. Install for previous versions of R >= 2.15:
+2. Install for previous versions of R >= 2.10:
 ```
-R CMD INSTALL Sushi_0.99.2.tar.gz
+R CMD INSTALL Sushi_1.0.1.tar.gz
 ```
 
 ## Contributors
@@ -35,4 +37,4 @@ R CMD INSTALL Sushi_0.99.2.tar.gz
 * Caros Araya
 
 ## License
-The code is freely available under the
+The code is freely available under the GPL (>= 2) license

vignettes/Figure_1.pdf

@@ -1,5 +1,5 @@
 library('Sushi')
-pdfname = "inst/doc/Figure_1.pdf"
+pdfname = "vignettes/Figure_1.pdf"
 Sushi_data = data(package = 'Sushi')
 data(list = Sushi_data$results[,3]) 
 makepdf = TRUE
@@ -452,7 +452,7 @@ chromstart       = 72998000
 chromend         = 73020000
 
 # plot gene structures
-plotGenes(Sushi_genes.bed, chrom, chromstart, chromend, maxrows=1, bheight=0.2, plotgenetype="arrow", bentline=FALSE, labeloffset=1, fontsize=1.2)
+plotGenes(Sushi_genes.bed, chrom, chromstart, chromend, maxrows=1, bheight=0.15, plotgenetype="arrow", bentline=FALSE, labeloffset=1, fontsize=1.2,arrowlength = 0.01)
 
 # label genome
 labelgenome(chrom, chromstart, chromend, n=3, scale="Mb")

vignettes/PaperFigure.R

@@ -1130,6 +1130,38 @@ if (file.exists("Rplots.pdf"))
 }
 @
 \end{center}
+
+\section{Tips}
+
+Other popular file formats such as BAM and GFF are not explicitly supported by Sushi.  However, data stored in these formats can be easily converted to BED format using common  command line tools such as the \texttt{bedtools} software suite available at \href{https://github.com/arq5x/bedtools2}{https://github.com/arq5x/bedtools2}.  Some examples taken from the \texttt{bedtools} are shown below. 
+
+\vspace{5 mm}
+Convert BAM alignments to BED format.
+
+\vspace{2 mm}
+\texttt{bamToBed -i reads.bam > reads.bed}
+
+\vspace{5 mm}
+Convert BAM alignments to BED format using edit distance (NM) as the BED \texttt{score}.
+
+\vspace{2 mm}
+\texttt{bamToBed -i reads.bam -ed > reads.bed}
+
+\vspace{5 mm}
+Convert BAM alignments to BEDPE format.
+
+\vspace{2 mm}
+\texttt{bamToBed -i reads.bam -bedpe > reads.bedpe}
+
+\vspace{5 mm}
+These BED files can easily be read into R for use with Sushi using the following R command:
+
+\begin{center}
+<<fig=FALSE, eval=FALSE ,echo=TRUE>>=
+read.table(file="reads.bed",sep="\t")
+@
+\end{center}
+
 \section{Appendix}
 
 For illustrative purposes we include a complex figure as published in the accompanying manuscript (Phanstiel, et al.).