Updated autoplot.dna_barplot help page

rDNA/NAMESPACE

@@ -3,6 +3,7 @@
 S3method(as.matrix,dna_network_onemode)
 S3method(as.matrix,dna_network_twomode)
 S3method(autoplot,dna_backbone)
+S3method(autoplot,dna_barplot)
 S3method(plot,dna_backbone)
 S3method(print,dna_backbone)
 S3method(print,dna_barplot)
@@ -21,15 +22,28 @@ export(dna_printDetails)
 export(dna_queryCoders)
 export(dna_sample)
 export(dna_saveConnectionProfile)
+importFrom(ggplot2,.pt)
 importFrom(ggplot2,aes_string)
+importFrom(ggplot2,annotate)
 importFrom(ggplot2,autoplot)
+importFrom(ggplot2,coord_flip)
+importFrom(ggplot2,element_blank)
+importFrom(ggplot2,element_text)
+importFrom(ggplot2,geom_bar)
 importFrom(ggplot2,geom_line)
+importFrom(ggplot2,geom_text)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,ggtitle)
+importFrom(ggplot2,position_stack)
+importFrom(ggplot2,scale_color_identity)
+importFrom(ggplot2,scale_fill_identity)
+importFrom(ggplot2,scale_x_discrete)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_bw)
+importFrom(ggplot2,theme_minimal)
 importFrom(ggplot2,xlab)
 importFrom(ggplot2,ylab)
+importFrom(grDevices,col2rgb)
 importFrom(graphics,lines)
 importFrom(rJava,.jarray)
 importFrom(rJava,.jcall)
@@ -43,4 +57,5 @@ importFrom(stats,filter)
 importFrom(utils,download.file)
 importFrom(utils,packageDescription)
 importFrom(utils,packageVersion)
+importFrom(utils,stack)
 importFrom(utils,unzip)

rDNA/R/rDNA.R

@@ -10,9 +10,9 @@ dnaEnvironment <- new.env(hash = TRUE, parent = emptyenv())
   packageStartupMessage(
     'Version:      ', desc$Version, '\n',
     'Date:         ', desc$Date, '\n',
-    'Author:        Philip Leifeld (University of Essex)\n',
-    'Contributors:  Tim Henrichsen (University of Warwick)\n',
-    '               Johannes B. Gruber (Vrije Universiteit Amsterdam),\n',
+    'Author:       Philip Leifeld (University of Essex)\n',
+    'Contributors: Tim Henrichsen (University of Warwick),\n',
+    '              Johannes B. Gruber (Vrije Universiteit Amsterdam)\n',
     'Project home: github.com/leifeld/dna'
   )
 }
@@ -1304,6 +1304,7 @@ as.matrix.dna_network_twomode <- as.matrix.dna_network_onemode
 #' plot(b)
 #' 
 #' # plot diagnostics with ggplot2
+#' library("ggplot2")
 #' p <- autoplot(b)
 #' p
 #'
@@ -1656,6 +1657,8 @@ autoplot.dna_backbone <- function(object, ..., ma = 500) {
 #' }
 #'
 #' @author Philip Leifeld
+#' 
+#' @seealso \link{print.dna_barplot}, \link{autoplot.dna_barplot}
 #'
 #' @importFrom rJava .jarray
 #' @importFrom rJava .jcall
@@ -1790,7 +1793,7 @@ dna_barplot <- function(statementType = "DNA Statement",
 #'
 #' @author Philip Leifeld
 #'
-#' @seealso \link{dna_barplot}
+#' @seealso \link{dna_barplot}, \link{autoplot.dna_barplot}
 #' @export
 print.dna_barplot <- function(x, trim = 30, attr = TRUE, ...) {
   x2 <- x
@@ -1813,27 +1816,29 @@ print.dna_barplot <- function(x, trim = 30, attr = TRUE, ...) {
 #'
 #' Plot a barplot generated from \code{\link{dna_barplot}}.
 #'
-#' This function plots \code{dna_barplot} objects generated by the 
-#' \code{\link{dna_barplot}} function. It plots agreement and disagreement with 
-#' DNA statements for different entities such as, e.g., \code{"concept"}, 
-#' \code{"organization"} or \code{"person"}. Colors can be modified before 
+#' This function plots \code{dna_barplot} objects generated by the
+#' \code{\link{dna_barplot}} function. It plots agreement and disagreement with
+#' DNA statements for different entities such as \code{"concept"},
+#' \code{"organization"}, or \code{"person"}. Colors can be modified before
 #' plotting (see examples).
 #' 
 #' @param object A \code{dna_barplot} object.
 #' @param lab.pos,lab.neg Names for (dis-)agreement labels.
 #' @param lab Should (dis-)agreement labels and title be displayed?
-#' @param colors If \code{TRUE}, the \code{Colors} column in the 
-#' \code{dna_barplot} object will be used to fill the bars. Also accepts 
-#' character objects matching one of the attribute variables of the 
-#' \code{dna_barplot} object.
-#' @param fontSize Text size in pts.
+#' @param colors If \code{TRUE}, the \code{Colors} column in the
+#'   \code{dna_barplot} object will be used to fill the bars. Also accepts
+#'   character objects matching one of the attribute variables of the
+#'   \code{dna_barplot} object.
+#' @param fontSize Text size in pt.
 #' @param barWidth Thickness of the bars. Bars will touch when set to \code{1}.
 #'   When set to \code{0.5}, space between two bars is the same as thickness of
 #'   bars.
 #' @param axisWidth Thickness of the x-axis which separates agreement from
 #'   disagreement.
-#' @param truncate Sets the number of characters to which axis labels should be truncated.
-#' @param exclude.min Reduces the plot to entities with a minimum frequency of statements.
+#' @param truncate Sets the number of characters to which axis labels should be
+#'   truncated.
+#' @param exclude.min Reduces the plot to entities with a minimum frequency of
+#'   statements.
 #'
 #' @examples
 #' \dontrun{
@@ -1847,36 +1852,29 @@ print.dna_barplot <- function(x, trim = 30, attr = TRUE, ...) {
 #'                  variable = "concept",
 #'                  qualifier = "agreement")
 #' 
-#' # plot barplot with ggplot2                
+#' # plot barplot with ggplot2
+#' library("ggplot2")
 #' autoplot(b)
 #' 
-#' ## Change barplot colors to other colors than specified in color attribute
-#' 
-#' # compute barplot data for organizations
+#' # use entity colours (here: colors of organizations as an illustration)
 #' b <- dna_barplot(statementType = "DNA Statement",
 #'                  variable = "organization",
 #'                  qualifier = "agreement")
-#'                  
-#' # Change color for NGOs to red
-#' b$Color[b$Type == "NGO"] <- "red"
-#' 
-#' # Change color for Government to blue
-#' b$Color[b$Type == "Government"] <- "blue"
+#' autoplot(b, colors = TRUE)
 #' 
+#' # edit the colors before plotting
+#' b$Color[b$Type == "NGO"] <- "red"         # change NGO color to red
+#' b$Color[b$Type == "Government"] <- "blue" # change government color to blue
 #' autoplot(b, colors = TRUE)
 #' 
-#' ## Use different color attribute and add colors using ggplot2
+#' # use an attribute, such as type, to color the bars
+#' autoplot(b, colors = "Type") +
+#'   scale_colour_manual(values = "black")
 #' 
-#' # compute barplot data for organizations
-#' b <- dna_barplot(statementType = "DNA Statement",
-#'                  variable = "organization",
-#'                  qualifier = "agreement")
-#'                  
-#' # Plot barplot with Type attribute and add three colors for the three 
-#' # organization types              
+#' # replace colors for the three possible actor types with custom colors
 #' autoplot(b, colors = "Type") +
-#'    scale_fill_manual(values = c("red", "blue", "green")) +
-#     scale_colour_manual(values = "black")
+#'   scale_fill_manual(values = c("red", "blue", "green")) +
+#'   scale_colour_manual(values = "black")
 #' }
 #'
 #' @author Johannes B. Gruber, Tim Henrichsen