R/make.clone.tree.grobs.R

In CancerEvolutionVisualization: Publication Quality Phylogenetic Tree Plots

make.clone.tree.grobs <- function(
    ccf.df,
    tree,
    scale1,
    scale2,
    wid,
    yat,
    default.branch.width,
    length.from.node.edge,
    seg1.col,
    seg2.col,
    cluster.list,
    add.polygons,
    sig.shape,
    spread,
    fixed.angle,
    add.node.text,
    text.df,
    node.text.line.dist,
    node.text.cex,
    text.on.nodes,
    yaxis.position,
    yaxis1.label,
    yaxis2.label,
    axis.label.cex,
    axis.cex,
    xaxis.label,
    min.width,
    draw.nodes,
    node.radius,
    label.nodes,
    node.col,
    label.cex,
    add.normal,
    normal.cex,
    main,
    main.cex,
    main.y,
    size.units,
    ...
    ) {

	#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), ];

	#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$length <- apply(
            tree,
            MARGIN = 1,
            FUN = function(x) {
                max(x[c(3, 6)]);
                }
            );
	} else {
	    tree$length <- tree$length1;
	    }

	if (draw.nodes != 'none' && 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);
    	}

	if (draw.nodes) {
	    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);
    }