v2.2.7

With joined plots, group labels and sorting, div lines were incorrectly printed causing plots to be misaligned. This has been resolved.

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: 2.2.6
-Date: 2018-05-02
+Version: 2.2.7
+Date: 2018-05-23
 Author: Roy Mathew Francis
 Authors@R: person("Roy", "Francis", email = "[email protected]",role = c("aut", "cre"))
 Maintainer: Roy Mathew Francis <[email protected]>

NEWS

@@ -1,3 +1,8 @@
+pophelper 2.2.7
+===========
+* 23-May-2018
+* With joined plots, group labels and sorting, div lines were incorrectly printed causing plots to be misaligned. This has been resolved.
+
 pophelper 2.2.6
 ===========
 * 02-May-2018

R/pophelper.R

@@ -1,8 +1,8 @@
 # Begin ------------------------------------------------------------------------
 
-# pophelper v2.2.6
+# pophelper v2.2.7
 # Functions
-# 02-May-2018
+# 23-May-2018
 
 # check packages
 pkgs <- c("Cairo","grid","gridExtra","ggplot2","gtable","tidyr")
@@ -2088,7 +2088,7 @@ grpLabels <- function(dframe=NULL,grplab=NA,selgrp=NA,subsetgrp=NA,ordergrp=FALS
   marker_position$divxpos <- marker_position$markerxpos+0.5
   # add runid
   marker_position$run <- runid
-  
+
   return(list(dframe=dfwork1,grplab=grplab1,label_position=label_position,
               marker_position=marker_position))
 }
@@ -2509,7 +2509,7 @@ sortInd <- function(dframe=NULL,grplab=NA,selgrp=NA,ordergrp=FALSE,sortind=NA,gr
 #' plotQ(qlist=slist[c(1,3)],sortind="all")
 #' plotQ(qlist=slist[c(1,3)],sortind="Cluster1")
 #' plotQ(qlist=slist[c(1,3)],sortind="label")
-#' plotQ(qlist=slist[c(1,3)],sortind="all",imgoutput="join")
+#' plotQ(qlist=slist[c(1,3)],sortind="all",imgoutput="join",sharedindlab=F)
 #' 
 #' # read group labels
 #' md <- read.delim(system.file("files/metadata.txt", package="pophelper"), header=T,stringsAsFactors=F)
@@ -2519,8 +2519,8 @@ sortInd <- function(dframe=NULL,grplab=NA,selgrp=NA,ordergrp=FALSE,sortind=NA,gr
 #' plotQ(qlist=slist[1:2],grplab=md[,2,drop=F],imgoutput="join")
 #' 
 #' # sort within groups
-#' plotQ(qlist=slist[1:2],grplab=md[,2,drop=F],imgoutput="join",sortind="all")
-#' plotQ(qlist=slist[1:2],grplab=md[,2,drop=F],imgoutput="join",sortind="Cluster1")
+#' plotQ(qlist=slist[1:2],grplab=md[,2,drop=F],imgoutput="join",sortind="all",sharedindlab=F)
+#' plotQ(qlist=slist[1:2],grplab=md[,2,drop=F],imgoutput="join",sortind="Cluster1",sharedindlab=F)
 #' plotQ(qlist=slist[1:2],grplab=md[,2,drop=F],imgoutput="join",sortind="label")
 #' 
 #' # reorder groups
@@ -3017,6 +3017,7 @@ plotQ <- function(qlist=NULL,imgoutput="sep",clustercol=NA,sortind=NA,grplab=NA,
       list_qlist <- vector("list",length=flen)
       list_grplab <- vector("list",length=flen)
     }
+    div_multiplier <- seq(from=0,to=(flen-1))
     for (i in seq_along(qlist))
     {
       fname <- names(qlist)[i]
@@ -3072,9 +3073,17 @@ plotQ <- function(qlist=NULL,imgoutput="sep",clustercol=NA,sortind=NA,grplab=NA,
       df1$ind <- as.character(rownames(df1))
       df1$run <- factor(rep(i,nrow(df1)))
       df1$order_ind <- seq(from=1,to=Ind)
-      order_cumulative <- seq(from=strt,to=(i*Ind))
-      df1$order_cumulative <- order_cumulative
-      strt <- (i*Ind)+1
+
+      # cumulative numbering
+      if(i==1) {
+        start <- 1
+        end <- Ind
+      }else{
+        start <- end+1
+        end <- Ind*i
+      }
+
+      df1$order_cumulative <- seq(from=start,to=end)
 
       # strip panel labelling
       if(any(is.na(splab)))
@@ -3102,16 +3111,11 @@ plotQ <- function(qlist=NULL,imgoutput="sep",clustercol=NA,sortind=NA,grplab=NA,
       if(grplabcheck)
       {
         div_position <- marker_position[c(marker_position$count %in% divgrp),]
-        div_position <- div_position[seq(from=2,to=(nrow(div_position)-1)),,drop=F]
+        div_position <- div_position[seq(from=2,to=(nrow(div_position)-1)),c("count","divxpos"),drop=F]
         div_position$run <- i
-        if(i>1 && sortindcheck!="label" && sortindcheck!="empty") 
-        {
-          div_position$divxpos <- div_position$divxpos+Ind
-          div_position$markerxpos <- div_position$markerxpos+Ind
-        }
+        if(sortindcheck!="label" && sortindcheck!="empty") div_position$divxpos <- div_position$divxpos+(Ind*div_multiplier[i])
         div_position_list[[i]] <- div_position
       }
-
       rm(df2)
     }
 
@@ -3170,7 +3174,7 @@ plotQ <- function(qlist=NULL,imgoutput="sep",clustercol=NA,sortind=NA,grplab=NA,
     # when ind labels are not shared, x-axis is free
     if(sharedindlab) gg_plot_panel <- gg_plot_panel+facet_wrap(~run,labeller=labeller(run=facetnames),strip.position=sppos,scales="fixed",nrow=flen,drop=TRUE)
     if(!sharedindlab) gg_plot_panel <- gg_plot_panel+facet_wrap(~run,labeller=labeller(run=facetnames),strip.position=sppos,scales="free_x",nrow=flen,drop=TRUE)
-
+    
     gg_plot_panel <- gg_plot_panel+
       labs(x=NULL,y=NULL)+
       theme(legend.position="top",
@@ -4526,7 +4530,7 @@ summarizeQ <- summariseQ
 
 #ON LOAD
 .onLoad <- function(...) {
-  packageStartupMessage("pophelper v2.2.6 ready.")
+  packageStartupMessage("pophelper v2.2.7 ready.")
 }
 
 # End --------------------------------------------------------------------------

README.md

@@ -1,4 +1,4 @@
-# pophelper 2.2.6
+# pophelper 2.2.7
 
 `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.  
 
@@ -63,4 +63,4 @@ The `pophelper` R package is offered free and without warranty of any kind, eith
 
 If you have an comments, suggestions, corrections or ideas on ways to improve or extend this package, feel free to contact me. Submit a report on the [Github issues page](https://github.com/royfrancis/pophelper/issues).  
 
-2018 Roy M Francis  
+2018 | Roy M Francis  

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 2.2.6",
+  note = "pophelper R package version 2.2.7",
   textVersion=
   paste("Francis, R. M. (2017).", 
   "pophelper: an R package and web app to analyse and visualize population structure.",

tests/testmanual/test-all.R

@@ -1,6 +1,6 @@
 # Test Script
-# v2.2.6
-# 02-May-2018
+# v2.2.7
+# 23-May-2018
 
 library(testthat)
 library(pophelper)
@@ -597,9 +597,15 @@ for(i in seq_along(imgout))
   #multiple labels
   plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs)
 
+  #multiple labels change selgrp
+  plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,selgrp="mixed")
+
   #multiple labels grpmean
   plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,grpmean=T)
 
+  #multiple labels grpmean change selgrp
+  plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,grpmean=T,selgrp="mixed")
+
   #multiple labels grpmean ordergrp
   plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,grpmean=T,ordergrp=T)
 
@@ -634,7 +640,7 @@ for(i in seq_along(imgout))
   plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,ordergrp=TRUE,sortind="label",showindlab=TRUE)
 
   #multiple labels grpmean
-  plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,grpmean=T)
+  plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,grpmean=T,showindlab=TRUE)
 
   #multiple labels grpmean showindlab
   plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,grpmean=T,showindlab=TRUE,width=15)
@@ -696,25 +702,25 @@ for(i in seq_along(imgout))
   if(imgo=="join")
   {
     #sharedindlab off
-    plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sharedindlab=F)
+    plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sharedindlab=F,outputfilename="joined")
     #sharedindlab on
-    plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sharedindlab=T)
+    plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sharedindlab=T,outputfilename="joined")
     #sharedindlab on with sort label
-    plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sharedindlab=T,sort="label")
+    plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sharedindlab=T,sort="label",outputfilename="joined")
     #sharedindlab with sort all
     expect_error(plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sortind="all"))
     #sharedindlab with sort cluster
     expect_error(plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sortind="Cluster1"))
     #sharedindlab off with grplab
-    plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sharedindlab=F,grplab=grplabs)
+    plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sharedindlab=F,grplab=grplabs,outputfilename="joined")
     #sharedindlab on with grplab
-    plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sharedindlab=T,grplab=grplabs,width=16)
+    plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sharedindlab=T,grplab=grplabs,width=16,outputfilename="joined")
     #shared indlab with repeated grplab
-    plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sharedindlab=T,grplab=grpsrep)
+    plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sharedindlab=T,grplab=grpsrep,outputfilename="joined")
     #sharedindlab with grplab subset
-    plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sharedindlab=T,grplab=grplabs,subsetgrp="a",width=16)
+    plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sharedindlab=T,grplab=grplabs,subsetgrp="a",width=16,outputfilename="joined")
     #sharedindlab with reorder
-    plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sharedindlab=T,grplab=grplabs,subsetgrp=c("b","a"),width=16)
+    plotQ(slist[1:2],imgoutput=imgo,showindlab=T,sharedindlab=T,grplab=grplabs,subsetgrp=c("b","a"),width=16,outputfilename="joined")
     #error sharedindlab error
     expect_error(plotQ(slist[1:2],imgoutput=imgo,grplab=grplabs,showindlab=T,sortind="Cluster1"))
     #error ordergrp error