v2.2.8.1

royfrancis · Mar 16, 2019 · a5ed339 · a5ed339
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,8 +2,8 @@ Package: pophelper
 Type: Package
 Title: Tabulate, analyse and visualise admixture proportions from STRUCTURE, TESS, BAPS, ADMIXTURE and tab-delimited q-matrices
     files
-Version: 2.2.8
-Date: 2019-03-15
+Version: 2.2.8.1
+Date: 2019-03-16
 Author: Roy Mathew Francis
 Authors@R: person("Roy", "Francis", email = "roy.m.francis@outlook.com",role = c("aut", "cre"))
 Maintainer: Roy Mathew Francis <roy.m.francis@outlook.com>
@@ -13,7 +13,7 @@ Description: A set of useful functions for processing admixture proportion files
     K using Evanno method, export clumpp files, export distruct files and generate barplots.
 URL: https://github.com/royfrancis/pophelper
 Depends:
-    R(>= 3.4.0),
+    R(>= 3.5.0),
     ggplot2
 Imports:
     grid,

diff --git a/NEWS b/NEWS
@@ -1,3 +1,11 @@
+pophelper 2.2.8.1
+===========
+* 16-Mar-2019
+* Fixed 'exportpath' issues in plotQ()
+* Added 'exportpath' to plotQMultiline() and evannoMethod()
+* Added 'exportpath' to tabulateQ()
+* Added 'exportpath' to summariseQ()
+
 pophelper 2.2.8
 ===========
 * 15-Mar-2019

diff --git a/R/pophelper.R b/R/pophelper.R
diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# pophelper 2.2.8
+# pophelper 2.2.8.1
 
 `pophelper` is an R package and web app to analyse and visualise population structure. `pophelper` curently supports output run files generated from population analysis programs such as STRUCTURE, TESS, TESS3, BAPS and numeric delimited formats such as ADMIXTURE or fastSTRUCTURE. The `pophelper` package can be used to read run files to R, tabulate runs, summarise runs, estimate *K* using the Evanno method, align clusters within K using CLUMPP, export files for DISTRUCT and generate barplot figures.  
 

diff --git a/inst/CITATION b/inst/CITATION
@@ -10,7 +10,7 @@ bibentry(bibtype = "Article",
   pages = "27-32",
   doi = "10.1111/1755-0998.12509",
   url = "https://github.com/royfrancis/pophelper",
-  note = "pophelper R package version 2.2.8",
+  note = "pophelper R package version 2.2.8.1",
   textVersion=
   paste("Francis, R. M. (2017).", 
   "pophelper: an R package and web app to analyse and visualize population structure.",

diff --git a/tests/testmanual/test-all.R b/tests/testmanual/test-all.R
@@ -1,6 +1,5 @@
 # Test Script
-# v2.2.8
-# 15-Mar-2018
+# v2.2.8.1
 
 library(testthat)
 library(pophelper)

diff --git a/vignettes/vignette.Rmd b/vignettes/vignette.Rmd
@@ -1,5 +1,5 @@
 ---
-title: "Pophelper 2.2.8"
+title: "Pophelper 2.2.8.1"
 output: 
   bookdown::html_document2: 
     code_folding: "none"
@@ -1643,7 +1643,7 @@ The argument `basesize` can be used to change text size of most text objects. Th
 
 __Exporting and returning__
 
-By default, when plotting, an image is exported into the working directory. This is the intended behaviour and the plot element sizes is tuned for export. Exporting can be turned off by `exportplot=FALSE`. By setting `returnplot=TRUE`, the plot object can be returned and saved as a variable for plotting later or further customisation. By setting `returndata=TRUE`, the internally processed data (qlist and grplab) can be returned to be saved to a variable. The returned object is a list and has the following structure:
+By default, when plotting, an image is exported into the working directory. This is the intended behaviour and the plot element sizes is tuned for export. A location other than the current working directory can be specified using `exportpath`. Exporting can be turned off by `exportplot=FALSE`. By setting `returnplot=TRUE`, the plot object can be returned and saved as a variable for plotting later or further customisation. By setting `returndata=TRUE`, the internally processed data (qlist and grplab) can be returned to be saved to a variable. The returned object is a list and has the following structure:
 
 ```
 $list
@@ -2035,7 +2035,7 @@ p <- plotQMultiline(slist[1],exportplot=F,returnplot=T)
 print(p)
 ```
 
-The returned object is a list with slots: plot and data. The plot slot contains a gtable plot object (result from gridExtra::arrangeGrob()) and the data slot contains two slots: qlist and grplab. The qlist contains the processed qlist and the grplab contains processed group labels. In the above example, only the plot slot is filled because only `returnplot=T` was used. The data is also returned if `returndata=T` is used.
+The returned object is a list with slots: plot and data. The plot slot contains a gtable plot object (result from gridExtra::arrangeGrob()) and the data slot contains two slots: qlist and grplab. The qlist contains the processed qlist and the grplab contains processed group labels. In the above example, only the plot slot is filled because only `returnplot=T` was used. The data is also returned if `returndata=T` is used. When exporting the image, a location other than the current working directory can be specified using `exportpath`.
 
 Note that this function can be slow and takes several minutes to run depending on number of individuals and number of files selected.
 
@@ -2082,7 +2082,7 @@ A schematic data structure of a two run 'qlist' would look like below:
 ```{r,eval=FALSE}
 $list
 +--$list
-+  +--$data.frame
+|  +--$data.frame
 +--$list
    +--$data.frame
 ```
@@ -2272,5 +2272,4 @@ The `pophelper` R package is offered free and without warranty of any kind, eith
 # Contact
 
 If you have any comments, suggestions or issues, report on the [Github issues page](https://github.com/royfrancis/pophelper/issues).  
-
-__End of Document.__  
+