Function to create scale bar

NEWS.md

@@ -9,6 +9,7 @@
 * Node-by-node control of node size
 * Aesthetic changes for heatmap and clone-genome distribution plot
 * Add parameters to specify polygon shape and width.
+* Add option to use scale bars instead of y-axes.
 
 ## Update
 * Fixed angle calculation bug where child angles do not follow

R/SRCGrob.R

@@ -27,7 +27,12 @@ SRCGrob <- function(
     polygon.shape = 3,
     polygon.width = 1.2,
     length.from.node.edge = TRUE,
-    size.units = 'npc'
+    size.units = 'npc',
+    scale.bar = FALSE,
+    scale.bar.coords = c(0.5, 1),
+    scale.size.1 = NA,
+    scale.size.2 = NA,
+    scale.padding = 1
     ) {
 
     add.node.text <- !is.null(node.text);
@@ -110,7 +115,12 @@ SRCGrob <- function(
         main = main,
         main.cex = main.cex,
         main.y = main.y,
-        size.units = size.units
+        size.units = size.units,
+        scale.bar = scale.bar,
+        scale.bar.coords = scale.bar.coords,
+        scale.size.1 = scale.size.1,
+        scale.size.2 = scale.size.2,
+        scale.padding = scale.padding
         );
 
     out.tree <- gTree(

R/calculate.clone.polygons.R

@@ -331,7 +331,6 @@ compute.clones <- function(
 	v <- v[is.na(v$parent) | v$parent != -1, ];
 	v <- rbind(root, v);
 	v <- count.leaves.per.node(v);
-
 	if (no.ccf) {
 	    tree$angle <- if ((is.null(fixed.angle) && nrow(v) > 6) || any(table(v$parent) > 2)) {
     		tau <- -(pi / 2.5);

R/make.clone.tree.grobs.R

@@ -37,42 +37,47 @@ make.clone.tree.grobs <- function(
     main.cex,
     main.y,
     size.units,
+    scale.bar,
+    scale.bar.coords,
+    scale.size.1,
+    scale.size.2,
+    scale.padding,
     ...
     ) {
 
-	#initializing dataframe for subclones
-	if ('excluded' %in% colnames(ccf.df)) {
-		v <- ccf.df[!ccf.df$excluded,];
-	} else {
-		v <- ccf.df;
-		v$excluded <- FALSE;
-	    }
-
-	v <- v[order(v$id), ];
-	no.ccf <- FALSE;
-
-	if (!('ccf' %in% colnames(ccf.df)) || all(is.na(ccf.df$ccf)) || add.polygons == FALSE) {
-	    v$vaf <- NULL;
-	    v$vaf[v$parent == -1] <- 1;
-	    no.ccf <- TRUE;
-	} else {
-	    v <- v[order(v$id),]
-	    v$vaf[!v$excluded] <- v$ccf[!v$excluded] / max(v$ccf[!v$excluded]);
-	    }
-
-	if (all(is.null(ccf.df$colour))) {
-	    v$colour <- node.col
-	    }
+    #initializing dataframe for subclones
+    if ('excluded' %in% colnames(ccf.df)) {
+        v <- ccf.df[!ccf.df$excluded,];
+    } else {
+        v <- ccf.df;
+        v$excluded <- FALSE;
+        }
+
+    v <- v[order(v$id), ];
+    no.ccf <- FALSE;
+
+    if (!('ccf' %in% colnames(ccf.df)) || all(is.na(ccf.df$ccf)) || add.polygons == FALSE) {
+        v$vaf <- NULL;
+        v$vaf[v$parent == -1] <- 1;
+        no.ccf <- TRUE;
+    } else {
+        v <- v[order(v$id),]
+        v$vaf[!v$excluded] <- v$ccf[!v$excluded] / max(v$ccf[!v$excluded]);
+        }
+
+    if (all(is.null(ccf.df$colour))) {
+        v$colour <- node.col
+        }
 
     extra.len <- if (no.ccf) node.radius else node.radius * 4;
 
-	v$x <- v$y <- v$len <- v$x.mid <- numeric(length(nrow(v)));
-	v <- v[order(v$tier, v$parent), ];
+    v$x <- v$y <- v$len <- v$x.mid <- numeric(length(nrow(v)));
+    v <- v[order(v$tier, v$parent), ];
 
-	#initializing line segment dataframe and adjusting lengths to accomodate the node circles
-	tree$angle <- numeric(length = nrow(tree));
-	tree$angle[tree$parent == -1] <- 0;
-	if ('length2' %in% colnames(tree)) {
+    #initializing line segment dataframe and adjusting lengths to accomodate the node circles
+    tree$angle <- numeric(length = nrow(tree));
+    tree$angle[tree$parent == -1] <- 0;
+    if ('length2' %in% colnames(tree)) {
         tree$length2.c <- tree$length2 / scale1 * scale2;
 
         tree$length <- apply(
@@ -82,103 +87,124 @@ make.clone.tree.grobs <- function(
                 max(x[c(3, 6)]);
                 }
             );
-	} else {
-	    tree$length <- tree$length1;
-	    }
-
-	if (length.from.node.edge == TRUE) {
-	    tree <- adjust.branch.lengths(v, tree, node.radius, scale1);
-    	}
-
-	extra.len <- extra.len * (1 / scale1);
-
-	clone.out <- make.clone.polygons(
-	    v,
-	    tree,
-	    wid,
-	    scale1,
-	    scale2,
-	    extra.len,
-	    node.col,
-	    spread = spread,
-	    sig.shape = sig.shape,
-	    fixed.angle = fixed.angle,
-	    add.polygons = add.polygons,
-	    no.ccf = no.ccf
-	    );
-
-	clone.out$no.ccf <- no.ccf;
-	plot.size <- calculate.main.plot.size(
-	    clone.out,
-	    scale1,
-	    wid,
-	    min.width,
-	    node.radius
-	    );
-
-	if (!no.ccf) {
-		get.CP.polygons(clone.out);
-    	}
-
-	add.tree.segs(clone.out, node.radius, default.branch.width, scale1, seg1.col, seg2.col);
-
-	if (!is.null(cluster.list)) {
-	    message(paste(
-	        'Clustered pie nodes will be supported in a future version.',
-	        'Plain nodes will be used.'
-	        ));
-	    # TODO Implement pie nodes
-		# add.pie.nodes(clone.out, node.radius, cluster.list);
-    	}
+    } else {
+        tree$length <- tree$length1;
+        }
+
+    if (length.from.node.edge == TRUE) {
+        tree <- adjust.branch.lengths(v, tree, node.radius, scale1);
+        }
+
+    extra.len <- extra.len * (1 / scale1);
+
+    clone.out <- make.clone.polygons(
+        v,
+        tree,
+        wid,
+        scale1,
+        scale2,
+        extra.len,
+        node.col,
+        spread = spread,
+        sig.shape = sig.shape,
+        fixed.angle = fixed.angle,
+        add.polygons = add.polygons,
+        no.ccf = no.ccf
+        );
+
+    clone.out$no.ccf <- no.ccf;
+    plot.size <- calculate.main.plot.size(
+        clone.out,
+        scale1,
+        wid,
+        min.width,
+        node.radius
+        );
+
+    if (!no.ccf) {
+        get.CP.polygons(clone.out);
+        }
+
+    add.tree.segs(clone.out, node.radius, default.branch.width, scale1, seg1.col, seg2.col);
+
+    if (!is.null(cluster.list)) {
+        message(paste(
+            'Clustered pie nodes will be supported in a future version.',
+            'Plain nodes will be used.'
+            ));
+        # TODO Implement pie nodes
+        # add.pie.nodes(clone.out, node.radius, cluster.list);
+        }
 
     add.node.ellipse(clone.out,node.radius, label.nodes, label.cex, scale1);
 
-	if (add.normal == TRUE) {
-		add.normal(clone.out,node.radius,label.cex, normal.cex)
-	    }
-
-	if (yaxis.position != 'none') {
-		add.axes(
-		    clone.out,
-		    yaxis.position,
-		    scale1 = scale1,
-		    scale2 = scale2,
-		    yat = yat,
-		    axis.label.cex = axis.label.cex,
-		    axis.cex = axis.cex,
-		    no.ccf = no.ccf,
-		    xaxis.label = xaxis.label,
-		    yaxis1.label = yaxis1.label,
-		    yaxis2.label = yaxis2.label
-		    );
-	    }
-
-	if (add.node.text == TRUE & !is.null(text.df)) {
-	    node.text.grobs <- add.text2(
-	        clone.out$tree,
-	        text.df,
-	        label.nodes = text.on.nodes,
-	        line.dist = node.text.line.dist,
-	        main.y = clone.out$height,
-	        panel.height = clone.out$height,
-	        panel.width = clone.out$width,
-	        xlims = clone.out$xlims,
-	        ymax = clone.out$ymax,
-	        cex = node.text.cex,
-	        v = clone.out$v,
-	        axis.type = yaxis.position,
-	        node.radius = node.radius,
-	        scale = scale1,
-	        clone.out = clone.out,
-	        alternating = FALSE
-	        );
-
-	    clone.out$grobs <- c(clone.out$grobs, list(node.text.grobs));
-	    }
-
-	if (!is.null(main)) {
-		add.main(clone.out, main, main.cex, main.y, size.units);
-    	}
-
-	return(clone.out);
+    if (add.normal == TRUE) {
+        add.normal(clone.out,node.radius,label.cex, normal.cex)
+        }
+
+    if (yaxis.position != 'none' & scale.bar == FALSE) {
+        add.axes(
+            clone.out,
+            yaxis.position,
+            scale1 = scale1,
+            scale2 = scale2,
+            yat = yat,
+            axis.label.cex = axis.label.cex,
+            axis.cex = axis.cex,
+            no.ccf = no.ccf,
+            xaxis.label = xaxis.label,
+            yaxis1.label = yaxis1.label,
+            yaxis2.label = yaxis2.label
+            );
+        }
+
+    if (scale.bar) {
+        scale.lengths <- prep.scale.length(
+            tree,
+            scale.size.1,
+            scale.size.2
+            );
+
+        add.scale.bar(
+            clone.out,
+            scale1,
+            scale2,
+            yaxis1.label = yaxis1.label,
+            yaxis2.label = yaxis2.label,
+            scale.length = scale.lengths,
+            main.cex = axis.label.cex$y,
+            label.cex = axis.cex$y,
+            pos = scale.bar.coords,
+            padding = scale.padding
+            );
+        }
+
+    if (add.node.text == TRUE & !is.null(text.df)) {
+        node.text.grobs <- add.text2(
+            clone.out$tree,
+            text.df,
+            label.nodes = text.on.nodes,
+            line.dist = node.text.line.dist,
+            main.y = clone.out$height,
+            panel.height = clone.out$height,
+            panel.width = clone.out$width,
+            xlims = clone.out$xlims,
+            ymax = clone.out$ymax,
+            cex = node.text.cex,
+            v = clone.out$v,
+            axis.type = yaxis.position,
+            node.radius = node.radius,
+            scale = scale1,
+            clone.out = clone.out,
+            alternating = FALSE
+            );
+
+        clone.out$grobs <- c(clone.out$grobs, list(node.text.grobs));
+        }
+
+    if (!is.null(main)) {
+        add.main(clone.out, main, main.cex, main.y, size.units);
+        }
+
+    return(clone.out);
     }