Added legendrow and legendspacing

royfrancis · Aug 14, 2019 · b8e7660 · b8e7660
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -3,7 +3,7 @@ Type: Package
 Title: Tabulate, analyse and visualise admixture proportions from STRUCTURE, TESS, BAPS, ADMIXTURE and tab-delimited q-matrices
     files
 Version: 2.3.0
-Date: 2019-08-11
+Date: 2019-08-14
 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>

diff --git a/NEWS.md b/NEWS.md
@@ -1,7 +1,7 @@
 # pophelper 2.3.0
 
 * 11-Aug-2019
-* Built on R-3.6.0
+* Built on R-3.6.0. Min req R-3.5.0.
 * Removed CLUMPP and DISTRUCT executables
 * 'useexe' argument in ClumppExport() deprecated.
 * Added alignK() function for label switching within and between K
@@ -13,6 +13,8 @@
 * Added function sortQ() to sort runs in a qlist by a run attribute
 * Added function mergeQ() to merge replicate runs within K
 * Added function splitQ() to split a qlist object by an attribute
+* 14-Aug-2019
+* Added arguments 'legendspacing' and 'legendrow' to plotQ()
 
 # pophelper 2.2.9
 

diff --git a/R/plot.R b/R/plot.R
@@ -686,6 +686,8 @@ sortInd <- function(dframe=NULL,grplab=NA,selgrp=NA,ordergrp=FALSE,sortind=NA,gr
 #' to 4.
 #' @param legendtextsize A numeric indicating size of the legend text. Defaults 
 #' to 3.
+#' @param legendspacing Spacing between legend items.
+#' @param legendrow Number of rows of legend.
 #' @param legendmargin A numeric vector of length 4 indicating top, right, 
 #' bottom and left margins of the legend.
 #' @param barsize A numeric indicating the width of the bars. Defaults to 1.
@@ -924,7 +926,7 @@ plotQ <- function(qlist=NULL,imgoutput="sep",clustercol=NA,sortind=NA,grplab=NA,
                   pointsize=NA,pointcol="grey30",pointbgcol="grey30",pointtype="|",pointalpha=1,
                   linepos=0.75,linesize=NA,linecol="grey30",linetype=1,linealpha=1,
                   showdiv=TRUE,divgrp=NA,divcol="white",divtype="21",divsize=0.25,divalpha=1,
-                  showlegend=FALSE,legendlab=NA,legendpos="right",legendkeysize=4,legendtextsize=3,legendmargin=c(0.5,0.5,0.5,0),
+                  showlegend=FALSE,legendlab=NA,legendpos="right",legendkeysize=4,legendtextsize=3,legendspacing=2,legendrow=NULL,legendmargin=c(0.5,0.5,0.5,0),
                   barsize=1,barbordersize=0,barbordercolour=NA,
                   showyaxis=FALSE,showticks=FALSE,ticksize=0.1,ticklength=0.03,
                   outputfilename=NA,imgtype="png",height=NA,width=NA,dpi=300,units="cm",
@@ -1154,6 +1156,7 @@ plotQ <- function(qlist=NULL,imgoutput="sep",clustercol=NA,sortind=NA,grplab=NA,
         scale_x_continuous(breaks=df2$order_ind,labels=df2$ind,expand=c(0,0))+
         scale_y_continuous(expand=c(0,0))+
         scale_fill_manual(values=coll,labels=legendlab1)+
+        guides(fill=guide_legend(nrow=legendrow,byrow=TRUE))+
         facet_wrap(~run,labeller=labeller(run=facetnames),strip.position=sppos,scales="fixed",nrow=1)+
         get(theme)(base_family=font,base_size=basesize)
 
@@ -1163,6 +1166,7 @@ plotQ <- function(qlist=NULL,imgoutput="sep",clustercol=NA,sortind=NA,grplab=NA,
               legend.title=element_blank(),
               legend.key.size=grid::unit(legendkeysize,"points"),
               legend.text=element_text(size=legendtextsize,colour=indlabcol),
+              legend.spacing.x=grid::unit(legendspacing,"points"),
               legend.spacing=grid::unit(0,"points"),
               legend.justification=legendpos,
               legend.margin=margin(legendmargin[1],legendmargin[2],legendmargin[3],legendmargin[4],"points"),
@@ -1543,13 +1547,15 @@ plotQ <- function(qlist=NULL,imgoutput="sep",clustercol=NA,sortind=NA,grplab=NA,
         scale_x_continuous(breaks=df3$order_ind,labels=df3$ind,expand=c(0,0))+
         scale_y_continuous(expand=c(0,0))+
         scale_fill_manual(values=coll,labels=legendlab1)+
+        guides(fill=guide_legend(nrow=legendrow,byrow=TRUE))+
         get(theme)(base_family=font,base_size=basesize)
     }else{
       gg_plot_panel <- ggplot2::ggplot(data=df3,aes(x=order_cumulative,y=value,fill=variable))+
         geom_bar(width=barsize,size=barbordersize,colour=barbordercolour,stat="identity",position="fill",na.rm=na.rm)+
         scale_x_continuous(breaks=df3$order_cumulative,labels=df3$ind,expand=c(0,0))+
         scale_y_continuous(expand=c(0,0))+
         scale_fill_manual(values=coll,labels=legendlab1)+
+        guides(fill=guide_legend(nrow=legendrow,byrow=TRUE))+
         get(theme)(base_family=font,base_size=basesize)
     }
 
@@ -1566,6 +1572,7 @@ plotQ <- function(qlist=NULL,imgoutput="sep",clustercol=NA,sortind=NA,grplab=NA,
             legend.title=element_blank(),
             legend.key.size=grid::unit(legendkeysize,"points"),
             legend.text=element_text(size=legendtextsize,colour=indlabcol),
+            legend.spacing.x=grid::unit(legendspacing,"points"),
             legend.spacing=grid::unit(0,"points"),
             legend.justification=legendpos,
             legend.margin=margin(legendmargin[1],legendmargin[2],legendmargin[3],legendmargin[4],"points"),

diff --git a/R/qlist.R b/R/qlist.R
@@ -5,7 +5,7 @@
 #' @param qlist A qlist object.
 #' @return Nothing.
 #' @details Returns error if the object is not a list, contents are not data.frames or NA list elements or missing run labels. Warnings are generated for non standard column labels or missing attributes 'ind' and 'k'. Warnings can be fixed by running \code{\link{as.qlist}}.
-#' @example 
+#' @examples 
 #' sfiles <- list.files(path=system.file("files/structure",package="pophelper"),
 #' full.names=TRUE)
 #' slist <- readQ(sfiles)

diff --git a/man/is.qlist.Rd b/man/is.qlist.Rd
diff --git a/man/plotQ.Rd b/man/plotQ.Rd
diff --git a/vignettes/index.Rmd b/vignettes/index.Rmd
@@ -39,7 +39,7 @@ fc <- captioner::captioner(prefix="Fig. ")
 
 This vignette/tutorial aims to demonstrate the use of R package `pophelper`. This package contains functions that are useful for processing output results from programs used in the analysis of population structure such as ADMIXTURE^1^, FASTSTRUCTURE^6^, STRUCTURE^5^, TESS^3^, BAPS^8^ and any q-matrix output as a numeric tabular delimited file.
 
-These softwares are popular programs used to discriminate populations, to determine population structure and to reveal the genetic composition of individuals using molecular markers. These programs generally use allelic frequency information to assign individuals to a pre-defined number of populations (*K*). The assignment is usually run for a range of *K* such as from *K*=2 to *K*=10. Multiple repeats are also usually carried out for each *K*. Each output file for each repeat of *K* showing the assignment probabilities of all individuals is referred to as the run file, cluster file or q-matrix file. `pophelper` has a set of functions that include reading into R, tabulating, summarising and plotting these run files. 
+These software are popular programs used to discriminate populations, to determine population structure and to reveal the genetic composition of individuals using molecular markers. These programs generally use allelic frequency information to assign individuals to a pre-defined number of populations (*K*). The assignment is usually run for a range of *K* such as from *K*=2 to *K*=10. Multiple repeats are also usually carried out for each *K*. Each output file for each repeat of *K* showing the assignment probabilities of all individuals is referred to as the run file, cluster file or q-matrix file. `pophelper` has a set of functions that include reading into R, tabulating, summarising and plotting these run files. 
 
 This vignette covers the use of all important functions in the `pophelper` package. The demonstration is ordered in the manner of a typical workflow. Input and output codes are printed in a font different from body text like `this`.  
 
@@ -816,7 +816,7 @@ sapply(slist1[c(1,3)],ncol)
 # modified for this document
 p1 <- plotQ(slist1[1],returnplot=T,exportplot=F,quiet=T,basesize=11,
             showlegend=T, legendlab=c("group1","group2"),
-            legendkeysize=10,legendtextsize=10,legendmargin=c(2,2,2,0))
+            legendkeysize=10,legendtextsize=10,legendmargin=c(2,2,2,0),legendrow=1)
 
 p2 <- plotQ(slist1[c(1,3)],imgoutput="join",returnplot=T,exportplot=F,quiet=T,basesize=11,
             showlegend=T, legendlab=c("group1","group2","group3"),