Add orientation parameter for genome labels

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BioCircos
 Title: Interactive Circular Visualization of Genomic Data using 'htmlwidgets' and 'BioCircos.js'
-Version: 0.3.3
+Version: 0.3.4
 Authors@R: c(person("Loan", "Vulliard", email = "lvulliard@cemm.at", role = c("trl", "cre")),
 	person("Xiaowei", "Chen", email = "chenxiaowei@moon.ibp.ac.cn", role = c("aut")),
 	person("Ya", "Cui", email = "cui_ya@163.com", role = c("aut")))
@@ -14,7 +14,7 @@ License: GPL-2 | file LICENSE
 Encoding: UTF-8
 URL: https://github.com/lvulliard/BioCircos.R
 LazyData: true
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.1
 Suggests: knitr, rmarkdown
 VignetteBuilder: knitr
 Imports: RColorBrewer, htmlwidgets, jsonlite, plyr, grDevices

R/BioCircos.R

@@ -29,9 +29,9 @@
 #' @param genomeTicksDisplay,genomeTicksLen,genomeTicksColor,genomeTicksTextSize,genomeTicksTextColor,genomeTicksScale
 #'  Should the refence genome have ticks, of which length, color (in hexadecimal RGB format), with labels in which font
 #' size and color, and spaced by how many bases?
-#' @param genomeLabelDisplay,genomeLabelTextSize,genomeLabelTextColor,genomeLabelDx,genomeLabelDy
+#' @param genomeLabelDisplay,genomeLabelTextSize,genomeLabelTextColor,genomeLabelDx,genomeLabelDy,genomeLabelOrientation
 #'  Should the reference genome have labels on each chromosome, in which font size and color? Moreover rotation
-#'  and radius shifts for the label texts can be adde
+#'  and radius shifts for the label texts can be added, and the angle between the radius and the label changed.
 #' 
 #' @param zoom Is zooming and moving in the visualization allowed?
 #' 
@@ -164,7 +164,7 @@ BioCircos <- function(tracklist = BioCircosTracklist(),
   genomeTicksDisplay = TRUE, genomeTicksLen = 5, genomeTicksColor = "#000", 
   genomeTicksTextSize = "0.6em", genomeTicksTextColor = "#000", genomeTicksScale = 30000000,
   genomeLabelDisplay = TRUE, genomeLabelTextSize = "10pt", genomeLabelTextColor = "#000",
-  genomeLabelDx = 0.028, genomeLabelDy = "-0.55em",
+  genomeLabelDx = 0.0, genomeLabelDy = 10, genomeLabelOrientation = 0,
   zoom = TRUE, TEXTModuleDragEvent = FALSE,
   SNPMouseOverDisplay = TRUE, SNPMouseOverColor = "#FF0000", SNPMouseOverCircleSize = 3,
   SNPMouseOverCircleOpacity = 0.9,
@@ -261,6 +261,7 @@ BioCircos <- function(tracklist = BioCircosTracklist(),
     genomeLabelTextColor = genomeLabelTextColor,
     genomeLabelDx = genomeLabelDx, 
     genomeLabelDy = genomeLabelDy,
+    genomeLabelOrientation = genomeLabelOrientation,
     SNPMouseEvent = T,
     SNPMouseClickDisplay = F,
     SNPMouseClickColor = "red",

README.md

@@ -45,6 +45,7 @@ Since the visualizations are powered by JavaScript, they are affected by the env
 * If nothing shows up in the Rstudio viewer pane, try displaying the plot you generated in your browser instead. You can export the figure using the *Save as Web Page...* option in the *Export* tab of the viewer pane.
 * If nothing shows up in a shiny application or an Rmarkdown document, try to update your web browser. 
 See the vignettes for examples of BioCircos plots that should be correctly displayed.
+* Rotation of labels using the *genomeLabelOrientation* parameter leads to a slight offset of the text when displayed in Firefox because some recent CSS options are not yet implemented.
 
 ### Obseved behavior
 
@@ -78,6 +79,7 @@ The following features have been added to the original BioCircos.js library, bas
 * Parameter *snp_value_maxmin_instance* set by *SNPsettings.range* when provided, to allow the use of a pre-defined range of values for the SNP track.
 * Similar parameters added for the range of Histogram/Bar tracks, Line tracks, CNV tracks and Heatmap tracks (for the range to be used for color mapping).
 * Parameter *opacity* added to each elements of SNP and Arc tracks.
+* Changes were made in order to allow rotation of genome labels with the new parameter *genomeLabelOrientation* and the radial offset *dy* is now directly integrated in the label translation.
 
 
 ## Contact

inst/htmlwidgets/BioCircos.js

@@ -451,7 +451,8 @@ HTMLWidgets.widget({
             textSize : opts.genomeLabelTextSize,
             textColor : opts.genomeLabelTextColor,
             dx : opts.genomeLabelDx,
-            dy : opts.genomeLabelDy
+            dy : opts.genomeLabelDy,
+            rotation : opts.genomeLabelOrientation
           },
           TEXTModuleDragEvent : opts.TEXTModuleDragEvent
         });

inst/htmlwidgets/lib/biocircos-1.1.2.js

@@ -628,7 +628,8 @@ var BioCircos;
              "textSize" : 15,
              "textColor" : "#000",
              "dx" : 0.028,
-             "dy" : "-0.55em"
+             "dy" : 15,
+             "rotation" : 0
           }
       };
 
@@ -761,6 +762,7 @@ var BioCircos;
       self.genomeTextColor=self.settings.genomeLabel.textColor;
       self.genomeTextDx=self.settings.genomeLabel.dx;
       self.genomeTextDy=self.settings.genomeLabel.dy;
+      self.genomeTextRotation=self.settings.genomeLabel.rotation;
 
       var labeli= self.genomeLabel.length;
       var initGenome = new Object();
@@ -1164,12 +1166,17 @@ var BioCircos;
 	    .each( function(d,i) { 
                d.angle = (d.startAngle + d.endAngle) / 2 - self.genomeTextDx;
                d.name = self.genomeLabel[i];
+               d.rotation = self.genomeTextRotation;
+               d.dy = self.genomeTextDy;
             })
-	    .attr("dy",self.genomeTextDy)
+      .attr("text-anchor", "middle") // Rotate around horizontal center of text box
+      .attr("alignment-baseline", "middle") // Rotate around vertical center of text box
+      .attr("vertical-align", "middle")
 	    .attr("transform", function(d){
-	       return "rotate(" + ( d.angle * 180 / Math.PI ) + ")" +
-	       "translate(0,"+ -1.0*(outerRadius+10) +")" +
-	       ( ( d.angle > Math.PI*2 && d.angle < Math.PI*0 ) ? "rotate(180)" : "");
+	       return "rotate(" + (d.angle * 180 / Math.PI ) + ")" +
+	       "translate(0,"+ -1.0*(outerRadius+10+d.dy) +")" +
+	       ( ( d.angle > Math.PI*2 && d.angle < Math.PI*0 ) ? "rotate(180)" : "") +
+         "rotate(" + d.rotation +")";
 	    })
 	    .text(function(d){
 	       return d.name;
@@ -1206,7 +1213,7 @@ var BioCircos;
 
         ticks.append("text")
             .attr("x", 8)
-            .attr("dy", ".35em")
+            .attr("dy", "0.35em")
             .style("font-size", self.ticksTextSize)
             .style("fill", self.ticksTextColor)
             .attr("transform", function(d) { return d.angle > Math.PI ? "rotate(180)translate(-16)" : null; })

vignettes/BioCircos.Rmd

@@ -7,7 +7,7 @@ output:
 vignette: >
   %\VignetteIndexEntry{BioCircos: Generating circular multi-track plots}
   %\VignetteEngine{knitr::rmarkdown}
-  \usepackage[utf8]{inputenc}
+  %\usepackage[utf8]{inputenc}
 date: "`r Sys.Date()`"
 author: "Loan Vulliard"
 ---