📚 🐎 Updated existing vignette to static version, compiled via R.rsp p…

…ackage. Added benchmarking vignette.

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: pasaR
 Type: Package
 Title: Pangenome Statistical Analysis for R
-Version: 0.0.9
+Version: 0.9.0
 Author: Stelios Batziakas
 Maintainer: Stelios Batziakas <ampatziakas@gmail.com>
 Description: Functions to read genome clustering results and allows
@@ -18,10 +18,11 @@ Imports: magrittr,
          gridExtra,
          stringi,
          stringr,
-         readr,
-         dendextend
+         readr
 RoxygenNote: 6.0.1
 Suggests: knitr,
+    micropan,
     rmarkdown,
-    micropan
-VignetteBuilder: knitr
+    dendextend,
+    R.rsp
+VignetteBuilder: R.rsp

README.md

@@ -4,7 +4,7 @@
 We present an R package, named pasaR, usable in the later stages of an pangenomic
 analysis, i.e. after the construction of the gene families for a given set of genomes, based on information of the full complement of gene families. A complete methodology is proposed, suitable for sets of genomes of varying complexity, optimizing and enriching an assortment of existing measures from micropan, the only R package currently available on CRAN for such studies. This is an on-going project so better documentantion, a more extensive vignette and additional functions will be added. However the package is fully functional.
 
-## Install package
+# Install package
 
 If package *devtools* is present, simply run:
 
@@ -13,6 +13,13 @@ library(devtools)
 install_github("ampatzia/PasaR")
 ```
 
+# Vignettes
+
+Currently there are available two vignettes for the package, both precompiled in pdf:
+
+* [Small case study and example of usage in a pangenome of 81 bacterial strains.] (https://github.com/ampatzia/pasaR/blob/master/vignettes/Pangenome_analysis_with_pasaR.pdf) .
+* [Benchmark comparison to package micropan] (https://github.com/ampatzia/pasaR/blob/master/vignettes/Benchmark_Comparison.pdf) .
+
 # Relevant publications
 
 Mpatziakas A, Psomopoulos FE, Moysiadis T and Sgardelis S. Computing pangenome statistics in R. F1000Research 2017, 6(ISCB Comm J):1529 (poster) ([doi: 10.7490/f1000research.1114765.1](http://dx.doi.org/10.7490/f1000research.1114765.1))

vignettes/Benchmark_Comparison.pdf.asis

@@ -0,0 +1,2 @@
+%\VignetteIndexEntry{Benchmark comparison}
+%\VignetteEngine{R.rsp::asis}

vignettes/Pangenome_analysis_with_pasaR.pdf.asis

@@ -0,0 +1,2 @@
+%\VignetteIndexEntry{Example of a Pangenome Statistical Analysis with pasaR}
+%\VignetteEngine{R.rsp::asis}