inst/doc/UserGuide.R

In CancerEvolutionVisualization: Publication Quality Phylogenetic Tree Plots

## ----echo=F, message=F--------------------------------------------------------
library(CancerEvolutionVisualization);

## ----echo=F-------------------------------------------------------------------
load('data/input.examples.Rda');

## ----echo=F-------------------------------------------------------------------
parent.only <- data.frame(tree.input[, 'parent', drop = FALSE]);

knitr::kable(
    parent.only,
    col.names = c(colnames(tree.input)[1]),
    row.names = TRUE
    );

## ----fig.show='hide'----------------------------------------------------------
parent.only.tree <- SRCGrob(parent.only);

## ----echo=F-------------------------------------------------------------------
grid.draw(parent.only.tree);

## ----echo=F-------------------------------------------------------------------
branch.lengths <- tree.input[, 1:3];

knitr::kable(
    branch.lengths,
    row.names = TRUE
    );

## ----fig.show='hide'----------------------------------------------------------
branch.lengths.tree <- SRCGrob(branch.lengths);

## ----fig.dim=c(5, 3.5)--------------------------------------------------------
grid.draw(branch.lengths.tree);

## ----echo=F-------------------------------------------------------------------
node.style <- tree.input[, c(
    'parent', 'length1', 'length2',
    'node.col', 'node.label.col',
    'border.col', 'border.width', 'border.type',
    'edge.col.1', 'edge.type.1',
    'edge.col.2', 'edge.width.2'
    )];

knitr::kable(
    node.style[, !(colnames(node.style) %in% c('parent', 'length1', 'length2'))],
    row.names = TRUE
    );

## ----fig.show='hide'----------------------------------------------------------
node.style.tree <- SRCGrob(node.style);

## ----fig.dim=c(5, 3.5), echo=F------------------------------------------------
grid.draw(node.style.tree);

## ----echo=F-------------------------------------------------------------------
CP <- tree.input[, c('parent', 'length1', 'length2', 'CP')];

knitr::kable(
    CP,
    row.names = TRUE
    );

## ----fig.show='hide'----------------------------------------------------------
CP.tree <- SRCGrob(CP);

## ----echo=F-------------------------------------------------------------------
grid.draw(CP.tree);

## ----echo=F-------------------------------------------------------------------
simple.text.data <- text.input[, 1:2];

knitr::kable(
    simple.text.data,
    col.names = colnames(text.input)[1:2]
    );

## ----fig.show='hide'----------------------------------------------------------
simple.text.tree <- SRCGrob(parent.only, simple.text.data);

## -----------------------------------------------------------------------------
grid.draw(simple.text.tree);

## ----echo=F-------------------------------------------------------------------
knitr::kable(
    text.input
    );

## ----fig.show='hide'----------------------------------------------------------
full.text.tree <- SRCGrob(parent.only, text.input);

## -----------------------------------------------------------------------------
grid.draw(full.text.tree);

## ----fig.show='hide'----------------------------------------------------------
padding.tree <- SRCGrob(
    branch.lengths,
    horizontal.padding = -0.8
    );

## ----fig.dim=c(3.5, 3.5)------------------------------------------------------
grid.draw(padding.tree);

## ----fig.show='hide'----------------------------------------------------------
scaled.tree <- SRCGrob(
    branch.lengths,
    scale1 = 1.5,
    scale2 = 0.5
    );

## ----fig.height=4-------------------------------------------------------------
grid.draw(scaled.tree);

## ----fig.show='hide'----------------------------------------------------------
title.tree <- SRCGrob(
    parent.only,
    main = 'Example Plot'
    );

## ----echo=F-------------------------------------------------------------------
title.tree$vp$y <- unit(0.8, 'npc');

## ----fig.height=3.5-----------------------------------------------------------
grid.draw(title.tree);

## ----fig.show='hide'----------------------------------------------------------
axis.title.tree <- SRCGrob(
    parent.only,
    yaxis1.label = 'SNVs',
    horizontal.padding = -0.6
    );

## ----echo=F-------------------------------------------------------------------
axis.title.tree$vp$x <- unit(0.75, 'npc');

## -----------------------------------------------------------------------------
grid.draw(axis.title.tree);

## ----fig.show='hide'----------------------------------------------------------
xaxis1.ticks <- c(10, 20, 30, 35, 40);
xaxis2.ticks <- c(100, 250, 400);

yat.tree <- SRCGrob(
    branch.lengths,
    yat = list(
        xaxis1.ticks,
        xaxis2.ticks
        ),
    horizontal.padding = -0.4
    );

## ----fig.width=5--------------------------------------------------------------
grid.draw(yat.tree);

## ----fig.show='hide'----------------------------------------------------------
normal.tree <- SRCGrob(
    parent.only,
    add.normal = TRUE
    );

## -----------------------------------------------------------------------------
grid.draw(normal.tree);