v2.2.9

BinaryFiles

@@ -1,8 +1,8 @@
-inst/bin/clumpp_linux_1.1.2b_32bit
-inst/bin/clumpp_linux_1.1.2b_64bit
-inst/bin/clumpp_mac_1.1.2b
-inst/bin/clumpp_windows_1.1.2b.exe
-inst/bin/distruct_linux_1.1_64bit
-inst/bin/distruct_macosx_1.1
-inst/bin/distruct_macosx_1.1_2013
-inst/bin/distruct_windows_1.1.exe
+inst/bin/clumpp_linux_1.1.2b_32bit
+inst/bin/clumpp_linux_1.1.2b_64bit
+inst/bin/clumpp_mac_1.1.2b
+inst/bin/clumpp_windows_1.1.2b.exe
+inst/bin/distruct_linux_1.1_64bit
+inst/bin/distruct_macosx_1.1
+inst/bin/distruct_macosx_1.1_2013
+inst/bin/distruct_windows_1.1.exe

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: 2.2.8.1
-Date: 2019-03-16
+Version: 2.2.9
+Date: 2019-04-14
 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>

NEWS

@@ -1,3 +1,8 @@
+pophelper 2.2.9
+===========
+* 14-Apr-2019
+* plotQ(): Order of runs in a joined plot was incorrect when k>10 and grplab in use. Fixed.
+
 pophelper 2.2.8.1
 ===========
 * 16-Mar-2019
@@ -9,7 +14,6 @@ pophelper 2.2.8.1
 pophelper 2.2.8
 ===========
 * 15-Mar-2019
-* R dependency set to >=3.5.0
 * Dropped dependency on package cairo
 * summariseQ() accepts single run tabulated input
 * evannoMethodStructure(): Argument 'file' incorrectly specified for pdf as 'filename'. Fixed

R/pophelper.R

@@ -1,6 +1,6 @@
 # Begin ------------------------------------------------------------------------
 
-# pophelper v2.2.8.1
+# pophelper v2.2.9
 # Functions
 
 # check packages
@@ -3077,7 +3077,7 @@ plotQ <- function(qlist=NULL,imgoutput="sep",clustercol=NA,sortind=NA,grplab=NA,
       k <- ncol(df1)
       Ind <- nrow(df1)
       df1$ind <- as.character(rownames(df1))
-      df1$run <- factor(rep(i,nrow(df1)))
+      df1$run <- as.integer(rep(i,nrow(df1)))
       df1$order_ind <- seq(from=1,to=Ind)
       df2 <- tidyr::gather(df1,"variable","value",-c(ind,run,order_ind))
 
@@ -3424,7 +3424,7 @@ plotQ <- function(qlist=NULL,imgoutput="sep",clustercol=NA,sortind=NA,grplab=NA,
       Ind <- nrow(df1)
       #df1$ind <- factor(rownames(df1),levels=rownames(df1))
       df1$ind <- as.character(rownames(df1))
-      df1$run <- factor(rep(i,nrow(df1)))
+      df1$run <- as.integer(rep(i,nrow(df1)))
       df1$order_ind <- seq(from=1,to=Ind)
 
       # cumulative numbering
@@ -5070,7 +5070,7 @@ summarizeQ <- summariseQ
 
 #ON LOAD
 .onLoad <- function(...) {
-  packageStartupMessage("pophelper v2.2.8.1 ready.")
+  packageStartupMessage("pophelper v2.2.9 ready.")
 }
 
 # End --------------------------------------------------------------------------

README.md

@@ -1,4 +1,4 @@
-# pophelper 2.2.8.1
+# pophelper 2.2.9
 
 `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.  
 

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 2.2.8.1",
+  note = "pophelper R package version 2.2.9",
   textVersion=
   paste("Francis, R. M. (2017).", 
   "pophelper: an R package and web app to analyse and visualize population structure.",