Spread x labels in densityplot

R/SRCGrob.R

@@ -41,6 +41,10 @@ SRCGrob <- function(
             ));
         }
 
+    if ('CCF' %in% colnames(tree) && !('CP' %in% colnames(tree))) {
+        tree$CP <- tree$CCF;
+        }
+
     add.node.text <- !is.null(node.text);
     add.polygons <- !is.null(tree$CP) && !disable.polygons;
     text.on.nodes <- FALSE;

R/create.ccf.densityplot.R

@@ -2,7 +2,6 @@ create.ccf.densityplot <- function(
     x,
     filename = NULL,
     clone.colours = NULL,
-    breaks = 100,
     xlab.label = 'CCF',
     ylab.label = 'SNV Density',
     xlimits = c(0, 1.5),
@@ -93,7 +92,7 @@ create.ccf.densityplot <- function(
         abline.col = 'gray50',
         add.text = TRUE,
         text.labels = lapply(mean.ccf$CCF, round, 2),
-        text.x = mean.ccf$CCF,
+        text.x = spread.values(mean.ccf$CCF, min.dist = legend.title.cex / 10),
         text.y = ymax,
         text.fontface = 'bold',
         text.cex = legend.title.cex
@@ -109,3 +108,26 @@ create.ccf.densityplot <- function(
         resolution = resolution
         ));
     }
+
+
+spread.values <- function(x, min.dist = 0.1, max.iter = 10) {
+    x.out <- x;
+    for (iter in seq_len(max.iter)) {
+        changed <- FALSE;
+        ord <- order(x.out);
+        x.sorted <- x.out[ord];
+
+        for (i in 2:length(x.sorted)) {
+            gap <- x.sorted[i] - x.sorted[i - 1];
+            if (gap < min.dist) {
+                shift <- (min.dist - gap) / 2;
+                x.sorted[i - 1] <- x.sorted[i - 1] - shift;
+                x.sorted[i]     <- x.sorted[i] + shift;
+                changed <- TRUE;
+            }
+        }
+        x.out[ord] <- x.sorted;
+        if (!changed) break;
+    };
+    return(x.out);
+}

R/set.up.plot.area.R

@@ -86,12 +86,18 @@ extend.axis <- function(axisGrob, limits, type) {
     }
 
 add.axis.label <- function(axisGrob, axis.label, axis.position, axis.label.cex, vp) {
+	axis.cex <- axisGrob$gp$cex;
     if (axis.position == 'bottom') {
         d <- 'y';
         just <- c('centre', 'top');
         rot <- 0;
         x <- unit(0.5, 'npc');
-        y <- (getGrob(axisGrob, 'labels')$y + getGrob(axisGrob, 'ticks')$y1) * 1.75;
+
+		y <- unit(
+			convertY(getGrob(axisGrob, 'labels')$y, 'mm', valueOnly = TRUE) -
+			convertY(unit(1.2, 'lines') * axis.cex, 'mm', valueOnly = TRUE),
+			'mm'
+			);
 	} else {
 		pushViewport(vp);
 
@@ -112,28 +118,28 @@ add.axis.label <- function(axisGrob, axis.label, axis.position, axis.label.cex,
 			d <- 'x';
 			just <- c('centre', 'centre');
 			rot <- 90;
-
-			x <- unit(
-			    convertX(grobWidth(getGrob(axisGrob, 'labels')), 'mm', valueOnly = TRUE) * -(axisGrob$gp$cex) -
-			        convertX(unit(1, 'lines') * axisGrob$gp$cex, 'mm', valueOnly = TRUE) +
-			        convertX(getGrob(axisGrob, 'labels')$x * axisGrob$gp$cex, 'mm', valueOnly = TRUE),
-			    'mm'
-			    );
+			sign <- -1;
 		} else if (axis.position == 'right') {
 			d <- 'x';
 			just <- c('left', 'centre');
 			x <- (getGrob(axisGrob, 'labels')$x + tick.length) * 1.5;
 			rot <- 270;
+			sign <- 1;
 		    }
 
-		popViewport()
+		x <- unit(
+			sign * (
+				convertX(grobWidth(getGrob(axisGrob, 'labels')), 'mm', valueOnly = TRUE) * axis.cex +
+				convertX(unit(1, 'lines') * axis.cex, 'mm', valueOnly = TRUE)
+				) +
+			convertX(getGrob(axisGrob, 'labels')$x, 'mm', valueOnly = TRUE), 'mm');
     	}
 
 	axis.lab <- textGrob(
 	    name = 'axis.label',
 	    axis.label,
 	    gp = gpar(cex = axis.label.cex),
-	    vjust = 0,
+	    vjust = 1,
 	    x = x,
 	    rot = rot,
 	    y = y
@@ -295,14 +301,14 @@ add.xaxis <- function(
 	    name = 'axis.content',
 	    at = xat,
 	    label = xlabels,
-	    gp = gpar(cex = axis.label.cex),
+	    gp = gpar(cex = axis.cex, vjust = 2),
 	    main = TRUE
 	    );
 
 	# Move the labels up slightly
 	xaxis.labels <- editGrob(
 	    getGrob(xaxis, 'labels'),
-	    y = unit(-0.09, 'npc'),
+		y = getGrob(xaxis, 'ticks')$y1 * 1.5,
 	    vjust = 1
 	    );
 

man/create.ccf.densityplot.Rd

@@ -9,7 +9,6 @@ create.ccf.densityplot(
     x,
     filename = NULL,
     clone.colours = NULL,
-    breaks = 100,
     xlab.label = 'CCF',
     ylab.label = 'SNV Density',
     xlimits = c(0, 1.5),
@@ -30,7 +29,6 @@ create.ccf.densityplot(
     \item{x}{A data-frame with the following column names: 'SNV.id', 'clone.id', 'CCF'.}
     \item{filename}{Filename for tiff output, or if NULL returns the trellis object itself. Defaults to \code{NULL}.}
     \item{clone.colours}{Named list to provide a colour scheme for the clone ID covariate bar. If NULL, colours will be randomly generated. Defaults to \code{NULL}.}
-    \item{breaks}{Number of breaks for the histogram. Defaults to 100.}
     \item{xlab.label}{Defaults to \dQuote{CCF}.}
     \item{ylab.label}{Defaults to \dQuote{SNV Density}.}
     \item{xlimits}{Limits for the x-axis. Defaults to \code{c(0, 1.5)}.}